1VJF | pdb_00001vjf

CRYSTAL STRUCTURE OF A PUTATIVE DNA-BINDING PROTEIN (CC_0111) FROM CAULOBACTER CRESCENTUS CB15 AT 1.62 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1VJF/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Caulobacter vibrioides CB15
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-02-11 Released: 2004-03-09 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.167 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Literature

Crystal structure of putative DNA-binding protein from Caulobacter crescentus at 1.62 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.

Macromolecule Content 

• Total Structure Weight: 20.25 kDa 
• Atom Count: 1,501 
• Modeled Residue Count: 168 
• Deposited Residue Count: 180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein, putative	A	180	Caulobacter vibrioides CB15	Mutation(s): 6
UniProt
Find proteins for Q9ABV9 (Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)) Explore Q9ABV9  Go to UniProtKB:  Q9ABV9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	B [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: 1.62 Å
• R-Value Free:  0.167 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VJF

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.891	α = 90
b = 50.891	β = 90
c = 121.43	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
CCP4	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-09 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-03-09
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-09
  Changes: Data collection, Structure summary