2PR7 | pdb_00002pr7

Crystal structure of uncharacterized protein (NP_599989.1) from Corynebacterium glutamicum ATCC 13032 Kitasato at 1.44 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2PR7/pdb

• Classification: HYDROLASE
• Organism(s): Corynebacterium glutamicum ATCC 13032
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-05-03 Released: 2007-05-15 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 
  0.199 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Crystal structure of uncharacterized protein (NP_599989.1) from Corynebacterium glutamicum ATCC 13032 Kitasato at 1.44 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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.51 kDa 
• Atom Count: 2,365 
• Modeled Residue Count: 274 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloacid dehalogenase/epoxide hydrolase family	A, B	137	Corynebacterium glutamicum ATCC 13032	Mutation(s): 2  Gene Names: NP_599989.1, cg0870

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	C [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 1.44 Å
• R-Value Free:  0.199 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32PR7

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.149	α = 100.72
b = 45.153	β = 103.86
c = 60.777	γ = 103.31

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-15 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-05-15
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-06
  Changes: Data collection, Refinement description, Structure summary