1VMF | pdb_00001vmf

CRYSTAL STRUCTURE OF a YBJQ-LIKE FOLD PROTEIN OF UNKNOWN FUNCTION (BH3498) FROM BACILLUS HALODURANS AT 1.46 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1VMF/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Halalkalibacterium halodurans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-09-23 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: 1.46 Å
• R-Value Free: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

Crystal structure of hypothetical protein (10176122) from Bacillus halodurans at 1.46 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 (software)

Macromolecule Content 

• Total Structure Weight: 50.26 kDa 
• Atom Count: 3,727 
• Modeled Residue Count: 407 
• Deposited Residue Count: 435 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein	A, B, C	145	Halalkalibacterium halodurans	Mutation(s): 0
UniProt
Find proteins for Q9K772 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9K772  Go to UniProtKB:  Q9K772

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	I [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
EDO	G [auth B], H [auth C], J [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	E [auth A], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VMF

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.601	α = 90
b = 58.951	β = 90
c = 134.964	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
SCALA	data scaling
SHELX	model building
SHARP	phasing
REFMAC	refinement
XDS	data reduction
CCP4	data scaling
SHELX	phasing

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, Version format compliance
• Version 1.3: 2017-12-20
  Changes: Database references
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations