4YME

Crystal structure of a sensory box/GGDEF family protein (CC_0091) from Caulobacter crescentus CB15 at 1.40 A resolution (PSI Community Target, Shapiro)

• PDB DOI: https://doi.org/10.2210/pdb4YME/pdb

• Classification: LYASE
• Organism(s): Caulobacter vibrioides CB15
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-06 Released: 2015-04-01 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG), Shapiro, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.205 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 

Literature

Crystal structure of a sensory box/GGDEF family protein (CC_0091) from Caulobacter crescentus CB15 at 1.40 A resolution (PSI Community Target, Shapiro)

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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16.77 kDa 
• Atom Count: 1,414 
• Modelled Residue Count: 156 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
sensory box/GGDEF family protein	A	158	Caulobacter vibrioides CB15	Mutation(s): 0  Gene Names: CC_0091
UniProt
Find proteins for Q9ABX9 (Caulobacter vibrioides (strain ATCC 19089 / CB15)) Explore Q9ABX9  Go to UniProtKB:  Q9ABX9

Small Molecules

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: 1.40 Å
• R-Value Free: 0.205 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M3RW2G

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.429	α = 90
b = 49.416	β = 90
c = 82.905	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XDS	data scaling
REFMAC	refinement
XSCALE	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-01 
Deposition Author(s): Joint Center for Structural Genomics (JCSG), Shapiro, L.

Revision History  

• Version 1.0: 2015-04-01
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-02-01
  Changes: Database references