1J6P | pdb_00001j6p

Crystal structure of Metal-dependent hydrolase of cytosinedemaniase/chlorohydrolase family (TM0936) from Thermotoga maritima at 1.9 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1J6P/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-07-09 Released: 2002-10-30 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.202 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Crystal structure of Metal-dependent hydrolase of cytosinedemaniase/chlorohydrolase family (TM0936) from Thermotoga maritima at 1.9 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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 48.09 kDa 
• Atom Count: 3,410 
• Modeled Residue Count: 407 
• Deposited Residue Count: 418 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METAL-DEPENDENT HYDROLASE OF CYTOSINEDEMANIASE/CHLOROHYDROLASE FAMILY	A	418	Thermotoga maritima	Mutation(s): 15  Gene Names: TM0936 EC: 3.5.4.31 (UniProt), 3.5.4.28 (UniProt)
UniProt
Find proteins for Q9X034 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X034  Go to UniProtKB:  Q9X034

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-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: 1.90 Å
• R-Value Free:  0.202 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31J6P

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.782	α = 90
b = 113.782	β = 90
c = 81.305	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling
CCP4	data reduction
SnB	phasing
MLPHARE	phasing
CCP4	model building
SOLVE	phasing
CNS	refinement
CCP4	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-10-30 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2002-10-30
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2018-07-18
  Changes: Advisory, Data collection, Database references
• Version 1.4: 2023-12-27
  Changes: Advisory, Data collection, Database references, Derived calculations
• Version 1.5: 2024-11-13
  Changes: Structure summary