7K3M

Crystal Structure of the Beta Lactamase Class D from Chitinophaga pinensis by Serial Crystallography

PDB DOI: https://doi.org/10.2210/pdb7K3M/pdb

Classification: HYDROLASE
Organism(s): Chitinophaga pinensis DSM 2588
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-09-11 Released: 2020-09-23
Deposition Author(s): Kim, Y., Sherrell, D.A., Johnson, J., Lavens, A., Maltseva, N., Endres, M., Babnigg, G., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.224
R-Value Work: 0.177
R-Value Observed: 0.183

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the Beta Lactamase Class D from Chitinophaga pinensis by Serial Crystallography

Kim, Y., Sherrell, D.A., Johnson, J., Lavens, A., Maltseva, N., Endres, M., Babnigg, G., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 29.88 kDa
Atom Count: 2,160
Modelled Residue Count: 245
Deposited Residue Count: 250
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	250	Chitinophaga pinensis DSM 2588	Mutation(s): 0 Gene Names: Cpin_0907 EC: 3.5.2.6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.224
R-Value Work: 0.177
R-Value Observed: 0.183
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.413	α = 90
b = 69.347	β = 90
c = 70.035	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CRISpy	data collection
DIALS	data reduction
PRIME	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-09-23

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2020-09-23
Type: Initial release
Version 1.1: 2020-10-28
Changes: Refinement description
Version 1.2: 2020-12-23
Changes: Database references, Structure summary
Version 1.3: 2024-04-03
Changes: Data collection, Database references, Refinement description

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.