3VNP | pdb_00003vnp

Crystal structure of hypothetical protein (GK2848) from Geobacillus Kaustophilus

• PDB DOI: https://doi.org/10.2210/pdb3VNP/pdb
• Entry: 3VNP supersedes: 2EG0

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Geobacillus kaustophilus HTA426
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-17 Released: 2012-03-07 
• Deposition Author(s): Karthe, P.P., Kumarevel, T.S., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.197 (DCC) 

Starting Model: experimental

Literature

Crystal structure of hypothetical protein (GK2848) from Geobacillus Kaustophilus

Karthe, P.P., Kumarevel, T.S., Kuramitsu, S., Yokoyama, S.

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: 60.38 kDa 
• Atom Count: 4,030 
• Modeled Residue Count: 513 
• Deposited Residue Count: 549 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical conserved protein	A, B, C	183	Geobacillus kaustophilus HTA426	Mutation(s): 0  Gene Names: GK2848 EC: 4.2.1.1
UniProt
Find proteins for Q5KW03 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KW03  Go to UniProtKB:  Q5KW03

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	D [auth A], F [auth B], H [auth C]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
MG	E [auth A], G [auth B], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.197 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.978	α = 90
b = 58.704	β = 90
c = 94.393	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-07 
Deposition Author(s): Karthe, P.P., Kumarevel, T.S., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
• This entry supersedes: 2EG0

Revision History  

• Version 1.0: 2012-03-07
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description