3LWD | pdb_00003lwd

Crystal structure of Putative 6-phosphogluconolactonase (YP_574786.1) from Chromohalobacter salexigens DSM 3043 at 1.88 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3LWD/pdb

• Classification: HYDROLASE
• Organism(s): Chromohalobacter israelensis DSM 3043
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-23 Released: 2010-04-07 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.186 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Literature

Crystal structure of Putative 6-phosphogluconolactonase (YP_574786.1) from Chromohalobacter salexigens DSM 3043 at 1.88 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 24.38 kDa 
• Atom Count: 2,043 
• Modeled Residue Count: 223 
• Deposited Residue Count: 226 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconolactonase	A	226	Chromohalobacter israelensis DSM 3043	Mutation(s): 0  Gene Names: Csal_2740 EC: 3.1.1.31
UniProt
Find proteins for Q1QTX1 (Chromohalobacter salexigens (strain ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11)) Explore Q1QTX1  Go to UniProtKB:  Q1QTX1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-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: 1.75 Å
• R-Value Free:  0.186 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33LWD

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.647	α = 90
b = 60.647	β = 90
c = 133.089	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-07 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-09
  Changes: Data collection, Structure summary