6NMO | pdb_00006nmo

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand SR-4

PDB DOI: https://doi.org/10.2210/pdb6NMO/pdb

Classification: LYASE
Organism(s): Burkholderia pseudomallei 1710b
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-01-11 Released: 2020-01-15
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.159 (Depositor), 0.160 (DCC)
R-Value Work:
0.126 (Depositor), 0.130 (DCC)
R-Value Observed:
0.127 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand SR-4.

Abendroth, J., Dranow, D.M., Pierce, P.G., Rouffet, M., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 52.84 kDa
Atom Count: 4,205
Modeled Residue Count: 478
Deposited Residue Count: 489
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	A, B, C	163	Burkholderia pseudomallei 1710b	Mutation(s): 0 Gene Names: ispF, BURPS1710b_2511 EC: 4.6.1.12
UniProt
Find proteins for Q3JRA0 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JRA0 Go to UniProtKB: Q3JRA0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3JRA0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QMS Query on QMS Download Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	N-(QUINOLIN-8-YL)METHANESULFONAMIDE C₁₀ H₁₀ N₂ O₂ S XYEPUTZVZYUENX-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain G [auth B]	F [auth A], G [auth B], K [auth B]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain K [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C]	D [auth A], H [auth B], L [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain L [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain N [auth C] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C]	I [auth B], J [auth B], N [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.159 (Depositor), 0.160 (DCC)
R-Value Work: 0.126 (Depositor), 0.130 (DCC)
R-Value Observed: 0.127 (Depositor)

Diffraction Data: https://doi.org/10.18430/m36nmo

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.08	α = 90
b = 67.6	β = 96.48
c = 60.81	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-01-15

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2020-01-15
Type: Initial release
Version 1.1: 2020-01-22
Changes: Database references, Structure summary
Version 1.2: 2020-03-11
Changes: Data collection, Database references
Version 1.3: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

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Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand SR-4

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand SR-4.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations