3CHV | pdb_00003chv

CRYSTAL STRUCTURE OF a prokaryotic domain of unknown function (DUF849) member (SPOA0042) FROM SILICIBACTER POMEROYI DSS-3 AT 1.45 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3CHV/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Ruegeria pomeroyi DSS-3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-10 Released: 2008-04-01 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.158 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

Literature

Crystal structure of prokaryotic domain of unknown function (DUF849) with a TIM barrel fold (YP_164873.1) from Silicibacter pomeroyi DSS-3 at 1.45 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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.55 kDa 
• Atom Count: 2,636 
• Modeled Residue Count: 279 
• Deposited Residue Count: 284 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prokaryotic domain of unknown function (DUF849) with a TIM barrel fold	A	284	Ruegeria pomeroyi DSS-3	Mutation(s): 0  Gene Names: YP_164873.1, SPOA0042
UniProt
Find proteins for Q6SJB6 (Ruegeria pomeroyi) Explore Q6SJB6  Go to UniProtKB:  Q6SJB6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.45 Å
• R-Value Free:  0.158 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33CHV

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.859	α = 90
b = 69.601	β = 94.19
c = 52.331	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-01 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-04-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-13
  Changes: Data collection, Structure summary