2O08 | pdb_00002o08

CRYSTAL STRUCTURE OF A PUTATIVE HD SUPERFAMILY HYDROLASE (BH1327) FROM BACILLUS HALODURANS AT 1.90 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb2O08/pdb

• Classification: HYDROLASE
• Organism(s): Halalkalibacterium halodurans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-11-27 Released: 2006-12-19 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.223 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Crystal structure of hypothetical protein (NP_242193.1) from Bacillus halodurans at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 45.76 kDa 
• Atom Count: 3,512 
• Modeled Residue Count: 374 
• Deposited Residue Count: 376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BH1327 protein	A, B	188	Halalkalibacterium halodurans	Mutation(s): 4  Gene Names: NP_242193.1 EC: 3.6.1.41
UniProt
Find proteins for Q9KD90 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KD90  Go to UniProtKB:  Q9KD90

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGI	O [auth B]	2'-DEOXYGUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 CIKGWCTVFSRMJU-KVQBGUIXSA-N
PG4	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], P [auth B], Q [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NO3	N [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
FE	C [auth A], D [auth A], L [auth B], M [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
UNL	F [auth A]	Unknown ligand VTLYFUHAOXGGBS-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: 1.90 Å
• R-Value Free:  0.223 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32O08

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.83	α = 90
b = 166.51	β = 90
c = 73.41	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SHARP	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-19 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.6: 2024-10-09
  Changes: Data collection, Refinement description, Structure summary