2PRR

Crystal structure of alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein (YP_296737.1) from Ralstonia eutropha JMP134 at 2.15 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein (YP_296737.1) from Ralstonia eutropha JMP134 at 2.15 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
197Cupriavidus pinatubonensis JMP134Mutation(s): 7 
Gene Names: YP_296737.1Reut_A2532
UniProt
Find proteins for Q46Y90 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197))
Explore Q46Y90 
Go to UniProtKB:  Q46Y90
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46Y90
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
CA [auth F],
FA [auth G],
IA [auth H],
P [auth B],
S [auth C],
CA [auth F],
FA [auth G],
IA [auth H],
P [auth B],
S [auth C],
W [auth D],
Y [auth E]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth E],
BA [auth E],
DA [auth F],
EA [auth F],
GA [auth G],
AA [auth E],
BA [auth E],
DA [auth F],
EA [auth F],
GA [auth G],
HA [auth G],
JA [auth H],
KA [auth H],
LA [auth I],
M [auth A],
MA [auth J],
N [auth A],
NA [auth J],
O [auth A],
OA [auth J],
PA [auth K],
Q [auth B],
QA [auth K],
R [auth B],
RA [auth L],
T [auth C],
U [auth C],
V [auth C],
X [auth D],
Z [auth E]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 1
  • Diffraction Data DOI: 10.18430/M32PRR Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.105α = 84.26
b = 93.953β = 81.64
c = 120.898γ = 77.73
Software Package:
Software NamePurpose
MolProbitymodel building
SHELXphasing
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2017-10-25
    Changes: Author supporting evidence