4RN3 | pdb_00004rn3

Crystal structure of a HAD-superfamily hydrolase, subfamily IA, variant 1 (GSU2069) from Geobacter sulfurreducens PCA at 2.15 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4RN3/pdb

• Classification: HYDROLASE
• Organism(s): Geobacter sulfurreducens PCA
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-10-22 Released: 2014-11-26 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.217 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Crystal structure of a HAD-superfamily hydrolase, subfamily IA, variant 1 (GSU2069) from Geobacter sulfurreducens PCA at 2.15 A resolution

Joint Center for Structural Genomics (JCSG)

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: 49.21 kDa 
• Atom Count: 3,417 
• Modeled Residue Count: 403 
• Deposited Residue Count: 426 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HAD superfamily hydrolase	A, B	213	Geobacter sulfurreducens PCA	Mutation(s): 2  Gene Names: GSU2069 EC: 3.1.3.18
UniProt
Find proteins for Q74BH2 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q74BH2  Go to UniProtKB:  Q74BH2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.217 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.469	α = 90
b = 190.593	β = 90
c = 40.866	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-26 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2014-11-26
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary