2O5A | pdb_00002o5a

Crystal structure of Q9KD89 from Bacillus halodurans. Northeast Structural Genomics target BhR21

• PDB DOI: https://doi.org/10.2210/pdb2O5A/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Halalkalibacterium halodurans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-12-05 Released: 2006-12-19 
• Deposition Author(s): Benach, J., Su, M., Seetharaman, J., Ho, C.H., Janjua, H., Cunningham, K., Ma, L.-C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.278 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.269 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Literature

Crystal structure of Q9KD89 from Bacillus halodurans. Northeast Structural Genomics target BhR21

Benach, J., Su, M., Seetharaman, J., Ho, C.H., Janjua, H., Cunningham, K., Ma, L.-C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.08 kDa 
• Atom Count: 1,769 
• Modeled Residue Count: 213 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BH1328 protein	A, B	125	Halalkalibacterium halodurans	Mutation(s): 2  Gene Names: BH1328
UniProt
Find proteins for Q9KD89 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KD89  Go to UniProtKB:  Q9KD89

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	C [auth A], D [auth A], E [auth A], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-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: 2.70 Å
• R-Value Free:  0.278 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.269 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.936	α = 90
b = 32.021	β = 90
c = 59.546	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
RESOLVE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SnB	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-19 
Deposition Author(s): Benach, J., Su, M., Seetharaman, J., Ho, C.H., Janjua, H., Cunningham, K., Ma, L.-C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2006-12-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-10-16
  Changes: Structure summary