2GF4

Crystal structure of Vng1086c from Halobacterium salinarium (Halobacterium halobium). Northeast Structural Genomics Target HsR14

• PDB DOI: https://doi.org/10.2210/pdb2GF4/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Halobacterium salinarum NRC-1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-03-21 Released: 2006-04-18 
• Deposition Author(s): Benach, J., Zhou, W., Jayaraman, S., Forouhar, F.F., Janjua, H., Xiao, R., Ma, L.-C., Cunningham, K., Wang, D., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.237 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

Crystal structure of Vng1086c from Halobacterium salinarium (Halobacterium halobium). Northeast Structural Genomics Target HsR14

Benach, J., Zhou, W., Jayaraman, S., Forouhar, F.F., Janjua, H., Xiao, R., Ma, L.-C., Cunningham, K., Wang, D., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 23.51 kDa 
• Atom Count: 1,455 
• Modelled Residue Count: 164 
• Deposited Residue Count: 200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Vng1086c	A, B	100	Halobacterium salinarum NRC-1	Mutation(s): 4  Gene Names: VNG1086C
UniProt
Find proteins for Q9HQM9 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)) Explore Q9HQM9  Go to UniProtKB:  Q9HQM9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	E [auth B], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth A], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.237 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.669	α = 90
b = 64.914	β = 90
c = 123.945	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-18 
Deposition Author(s): Benach, J., Zhou, W., Jayaraman, S., Forouhar, F.F., Janjua, H., Xiao, R., Ma, L.-C., Cunningham, K., Wang, D., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2006-04-18
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary