6WGP | pdb_00006wgp

The crystal structure of a beta lactamase from Xanthomonas campestris pv. campestris str. ATCC 33913

• PDB DOI: https://doi.org/10.2210/pdb6WGP/pdb

• Classification: HYDROLASE
• Organism(s): Xanthomonas campestris pv. campestris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-06 Released: 2020-04-29 
• Deposition Author(s): Tan, K., Wu, R., Endres, M., 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: 1.50 Å
• R-Value Free: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of a beta lactamase from Xanthomonas campestris pv. campestris str. ATCC 33913

Tan, K., Wu, R., Endres, M., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.04 kDa 
• Atom Count: 2,280 
• Modeled Residue Count: 268 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	274	Xanthomonas campestris pv. campestris	Mutation(s): 0  Gene Names: bla, D0A42_09675 EC: 3.5.2.6
UniProt
Find proteins for H9AXM7 (Xanthomonas campestris pv. campestris) Explore H9AXM7  Go to UniProtKB:  H9AXM7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	B [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	C [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.262	α = 90
b = 66.894	β = 112.656
c = 43.895	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SBC-Collect	data collection
HKL-3000	phasing
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-29 
Deposition Author(s): Tan, K., Wu, R., Endres, M., Joachimiak, A., 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	HHSN272201700060C

Revision History  

• Version 1.0: 2020-04-29
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-10-23
  Changes: Structure summary