5TV7

2.05 Angstrom Resolution Crystal Structure of Peptidoglycan-Binding Protein from Clostridioides difficile in Complex with Glutamine Hydroxamate.

PDB DOI: https://doi.org/10.2210/pdb5TV7/pdb

Classification: HYDROLASE
Organism(s): Clostridioides difficile 630
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-11-08 Released: 2016-12-14
Deposition Author(s): Minasov, G., Wawrzak, Z., Shuvalova, L., Winsor, J., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.210
R-Value Work: 0.172
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

2.05 Angstrom Resolution Crystal Structure of Peptidoglycan-Binding Protein from Clostridioides difficile in Complex with Glutamine Hydroxamate.

Minasov, G., Wawrzak, Z., Shuvalova, L., Winsor, J., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 39.82 kDa
Atom Count: 2,758
Modelled Residue Count: 316
Deposited Residue Count: 356
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative peptidoglycan-binding/hydrolysing protein	A, B	178	Clostridioides difficile 630	Mutation(s): 0 Gene Names: CD630_23880
UniProt
Find proteins for Q181X4 (Clostridioides difficile (strain 630)) Explore Q181X4 Go to UniProtKB: Q181X4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q181X4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HGA Query on HGA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	GLUTAMINE HYDROXAMATE C₅ H₁₀ N₂ O₄ YVGZXTQJQNXIAU-VKHMYHEASA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.210
R-Value Work: 0.172
R-Value Observed: 0.173
Space Group: C 1 2 1
Diffraction Data: https://doi.org/10.18430/m35tv7

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.949	α = 90
b = 35.008	β = 126.25
c = 101.533	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-12-14

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-12-14
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.