1VMH | pdb_00001vmh

Crystal structure of an uncharacterized conserved protein yjbq/upf0047 family, ortholog yugu b.subtilis (ca_c0907) from clostridium acetobutylicum at 1.31 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VMH/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Clostridium acetobutylicum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-09-24 Released: 2004-10-05 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Uncharacterized conserved protein YjbQ/UPF0047 family, ortholog yugU B.subtilis (15023806) from Clostridium acetobutylicum at 1.31 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 16.1 kDa 
• Atom Count: 1,171 
• Modeled Residue Count: 129 
• Deposited Residue Count: 144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized conserved protein YjbQ/UPF0047 family, ortholog yugU B.subtilis	A	144	Clostridium acetobutylicum	Mutation(s): 0  Gene Names: CAC0907
UniProt
Find proteins for Q97KL0 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)) Explore Q97KL0  Go to UniProtKB:  Q97KL0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VMH

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.406	α = 90
b = 79.406	β = 90
c = 50.688	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-05 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-10-05
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description