2PRR

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

• PDB DOI: https://doi.org/10.2210/pdb2PRR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cupriavidus pinatubonensis JMP134
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-05-04 Released: 2007-05-29 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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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 

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.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration, light scattering

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content

• Total Structure Weight: 272.91 kDa 
• Atom Count: 19,292 
• Modelled Residue Count: 2,276 
• Deposited Residue Count: 2,364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein	A, B, C, D, E, F, G, H, I, J, K, L	197	Cupriavidus pinatubonensis JMP134	Mutation(s): 7  Gene Names: YP_296737.1, Reut_A2532
UniProt
Find proteins for Q46Y90 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)) Explore Q46Y90  Go to UniProtKB:  Q46Y90

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	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
PEG	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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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: https://doi.org/10.18430/M32PRR

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.105	α = 84.26
b = 93.953	β = 81.64
c = 120.898	γ = 77.73

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-29 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• 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
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.6: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary