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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.31 Å
R-Value Free:
0.185 (Depositor), 0.191 (DCC)
R-Value Work:
0.157 (Depositor), 0.168 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97KL0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.31 Å
R-Value Free: 0.185 (Depositor), 0.191 (DCC)
R-Value Work: 0.157 (Depositor), 0.168 (DCC)
R-Value Observed: 0.159 (Depositor)

Diffraction Data:

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

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Entry History

Deposition Data

Released Date: 2004-10-05

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.