9C1C | pdb_00009c1c

Mycobacterium tuberculosis PKS13 acyltransferase serine converted to beta-lactam form by CEC215 via SuFEx reaction

PDB DOI: https://doi.org/10.2210/pdb9C1C/pdb

Classification: ANTIBIOTIC
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-29 Released: 2025-05-21
Deposition Author(s): Tang, S., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Welch Foundation, Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free:
0.235 (Depositor), 0.236 (DCC)
R-Value Work:
0.191 (Depositor), 0.198 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Mycobacterium tuberculosis PKS13 acyltransferase serine converted to beta-lactam form by CEC215 via SuFEx reaction

Tang, S., Sacchettini, J.C.

To be published.

Macromolecule Content

Total Structure Weight: 162.96 kDa
Atom Count: 7,669
Modeled Residue Count: 947
Deposited Residue Count: 1,473
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyketide synthase Pks13	A	491	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: pks13, Rv3800c EC: 2.3.1
UniProt
Find proteins for I6X8D2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6X8D2 Go to UniProtKB: I6X8D2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I6X8D2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyketide synthase Pks13	B, C [auth D]	491	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: pks13, Rv3800c EC: 2.3.1
UniProt
Find proteins for I6X8D2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6X8D2 Go to UniProtKB: I6X8D2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I6X8D2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain CA [auth A] MOL2 format, chain CA [auth A] mmCIF format, chain CA [auth A]	CA [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Interactions & Density Focus chain CA [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain UA [auth B] SDF format, chain VA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain VA [auth B]	UA [auth B], VA [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain UA [auth B] Focus chain VA [auth B] Interactions & Density Focus chain UA [auth B] Focus chain VA [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain ZA [auth D] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain ZA [auth D] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain ZA [auth D]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], ZA [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain ZA [auth D] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain ZA [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain FA [auth A] SDF format, chain XA [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain XA [auth B] mmCIF format, chain FA [auth A] mmCIF format, chain XA [auth B]	FA [auth A], XA [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain FA [auth A] Focus chain XA [auth B] Interactions & Density Focus chain FA [auth A] Focus chain XA [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain EA [auth A] MOL2 format, chain EA [auth A] mmCIF format, chain EA [auth A]	EA [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Interactions & Density Focus chain EA [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain GA [auth A] SDF format, chain WA [auth B] SDF format, chain YA [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain YA [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain YA [auth B]	DA [auth A], GA [auth A], WA [auth B], YA [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth A] Focus chain GA [auth A] Focus chain WA [auth B] Focus chain YA [auth B] Interactions & Density Focus chain DA [auth A] Focus chain GA [auth A] Focus chain WA [auth B] Focus chain YA [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AA [auth A] BA [auth A] OA [auth B] PA [auth B] QA [auth B] AA [auth A], BA [auth A], OA [auth B], PA [auth B], QA [auth B], RA [auth B], SA [auth B], T [auth A], TA [auth B], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.235 (Depositor), 0.236 (DCC)
R-Value Work: 0.191 (Depositor), 0.198 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.524	α = 90
b = 106.524	β = 90
c = 258.644	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-21

Deposition Author(s):

Tang, S.

Sacchettini, J.C.

TB Structural Genomics Consortium (TBSGC)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01AI095208
Welch Foundation	United States	A-0015
Bill & Melinda Gates Foundation	United States	INV-040487