2O08 | pdb_00002o08

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.223 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2O08

Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history. 

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.

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

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BH1327 protein
A, B
188Halalkalibacterium haloduransMutation(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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KD90
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGI

Query on DGI


Download:Ideal Coordinates CCD File
O [auth B]2'-DEOXYGUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
CIKGWCTVFSRMJU-KVQBGUIXSA-N
PG4

Query on PG4


Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
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

Query on PO4


Download:Ideal Coordinates CCD File
E [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
NO3

Query on NO3


Download:Ideal Coordinates CCD File
N [auth B]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
FE

Query on FE


Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
L [auth B],
M [auth B]		FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
UNL

Query on UNL


Download:Ideal Coordinates CCD File
F [auth A]Unknown ligand
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.223 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.83α = 90
b = 166.51β = 90
c = 73.41γ = 90
Software Package:
Software NamePurpose
MolProbitymodel building
SHARPphasing
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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