3H3Z | pdb_00003h3z

Crystal structure of a putative cyclic nucleotide binding protein (spoa0323) from ruegeria pomeroyi dss-3 at 2.35 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3H3Z/pdb

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


• Deposited: 2009-04-17 Released: 2009-05-05 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.236 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Crystal structure of PUTATIVE CAMP-BINDING REGULATORY PROTEIN (YP_165150.1) from SILICIBACTER POMEROYI DSS-3 at 2.35 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 52.45 kDa 
• Atom Count: 3,588 
• Modeled Residue Count: 454 
• Deposited Residue Count: 470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic nucleotide-binding protein	A, B	235	Ruegeria pomeroyi DSS-3	Mutation(s): 0  Gene Names: SPOA0323, YP_165150.1
UniProt
Find proteins for Q5LKQ8 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LKQ8  Go to UniProtKB:  Q5LKQ8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 2.35 Å
• R-Value Free:  0.236 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33H3Z

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.052	α = 90
b = 137.052	β = 90
c = 94.937	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
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: 2009-05-05 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, 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: 2024-11-27
  Changes: Data collection, Structure summary