6NIQ | pdb_00006niq

Crystal Structure of the Putative Class A Beta-Lactamase PenP from Rhodopseudomonas palustris

• PDB DOI: https://doi.org/10.2210/pdb6NIQ/pdb

• Classification: HYDROLASE
• Organism(s): Rhodopseudomonas palustris CGA009
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-12-31 Released: 2019-01-16 
• Deposition Author(s): Kim, Y., Tesar, C., 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.176 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Putative Class A Beta-Lactamase PenP from Rhodopseudomonas palustris

Kim, Y., Tesar, C., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 56.48 kDa 
• Atom Count: 4,498 
• Modeled Residue Count: 524 
• Deposited Residue Count: 534 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	267	Rhodopseudomonas palustris CGA009	Mutation(s): 0  Gene Names: penA, penP, RPA0362 EC: 3.5.2.6
UniProt
Find proteins for Q6NCV7 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NCV7  Go to UniProtKB:  Q6NCV7

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	C [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	F [auth A], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	E [auth A], J [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	G [auth A], H [auth A], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.176 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.608	α = 90
b = 69.711	β = 90
c = 112.505	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Kim, Y., Tesar, C., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description