5VPQ | pdb_00005vpq

Crystal structure of beta-lactamase from Burkholderia phymatum

• PDB DOI: https://doi.org/10.2210/pdb5VPQ/pdb

• Classification: HYDROLASE
• Organism(s): Paraburkholderia phymatum STM815
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-05-05 Released: 2017-05-17 
• Deposition Author(s): SSGCID, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.161 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of beta-lactamase from Burkholderia phymatum

Conrady, D.G., Delker, S.L., Lorimer, D.D., Edwards, T.E.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.47 kDa 
• Atom Count: 5,116 
• Modeled Residue Count: 547 
• Deposited Residue Count: 578 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	289	Paraburkholderia phymatum STM815	Mutation(s): 0  Gene Names: Bphy_2229 EC: 3.5.2.6
UniProt
Find proteins for B2JET9 (Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815)) Explore B2JET9  Go to UniProtKB:  B2JET9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	G [auth A], H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	C [auth A], D [auth A], E [auth A], F [auth A], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.161 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35VPQ

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.7	α = 90
b = 165.61	β = 90
c = 73.92	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-17 
Deposition Author(s): SSGCID, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-05-17
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description