9CCR | pdb_00009ccr

Crystal structure of the EspE7 thioesterase mutant R35A from the esperamicin biosynthetic pathway at 1.6 A

PDB DOI: https://doi.org/10.2210/pdb9CCR/pdb

Classification: HYDROLASE
Organism(s): Actinomadura verrucosospora
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-06-23 Released: 2025-06-25
Deposition Author(s): Miller, M.D., Hankore, E.D., Xu, W., Kosgei, A.J., Bhardwaj, M., Thorson, J.S., Van Lanen, S.G., Phillips Jr., G.N.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.203 (Depositor), 0.204 (DCC)
R-Value Work:
0.177 (Depositor), 0.179 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Functional and structural studies on the esperamicin thioesterase and progress toward understanding enediyne core biosynthesis

Hankore, E.D., Miller, M.D., Kosgei, A.J., Xu, W., Tan, K., Endres, M., Bhardwaj, M., Joachimiak, G., Joachimiak, A., Phillips Jr., G.N., Thorson, J.S., Van Lanen, S.G.

To be published.

Macromolecule Content

Total Structure Weight: 84.89 kDa
Atom Count: 5,013
Modeled Residue Count: 562
Deposited Residue Count: 720
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioesterase	A, B, C, D	180	Actinomadura verrucosospora	Mutation(s): 1 Gene Names: EspE7
UniProt
Find proteins for A0A2D0TCG5 (Actinomadura verrucosospora) Explore A0A2D0TCG5 Go to UniProtKB: A0A2D0TCG5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2D0TCG5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DCC Query on DCC Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain H [auth B]	F [auth A], H [auth B], J [auth C], L [auth D]	DODECYL-COA C₃₃ H₅₈ N₇ O₁₇ P₃ S YMCXGHLSVALICC-GMHMEAMDSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.203 (Depositor), 0.204 (DCC)
R-Value Work: 0.177 (Depositor), 0.179 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.769	α = 90
b = 90.055	β = 90
c = 95.718	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
DIALS	data scaling
DIALS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-25

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM115261
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01-CA217255
National Science Foundation (NSF, United States)	United States	STC-1231306