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)

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 1.5 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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q46Y90
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain FA [auth G] SDF format, chain W [auth D] SDF format, chain Y [auth E] SDF format, chain IA [auth H] SDF format, chain P [auth B] SDF format, chain S [auth C] MOL2 format, chain CA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain IA [auth H] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C]	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		Interactions Focus chain CA [auth F] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain P [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain Y [auth E] Interactions & Density Focus chain CA [auth F] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain P [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain Y [auth E]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain GA [auth G] SDF format, chain HA [auth G] SDF format, chain JA [auth H] SDF format, chain KA [auth H] SDF format, chain LA [auth I] SDF format, chain M [auth A] SDF format, chain MA [auth J] SDF format, chain N [auth A] SDF format, chain NA [auth J] SDF format, chain O [auth A] SDF format, chain OA [auth J] SDF format, chain PA [auth K] SDF format, chain QA [auth K] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain X [auth D] SDF format, chain Z [auth E] SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain EA [auth F] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain RA [auth L] SDF format, chain T [auth C] MOL2 format, chain DA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain KA [auth H] MOL2 format, chain LA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth J] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth J] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth J] MOL2 format, chain PA [auth K] MOL2 format, chain QA [auth K] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth L] MOL2 format, chain T [auth C]	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		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth J] Focus chain N [auth A] Focus chain NA [auth J] Focus chain O [auth A] Focus chain OA [auth J] Focus chain PA [auth K] Focus chain Q [auth B] Focus chain QA [auth K] Focus chain R [auth B] Focus chain RA [auth L] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth J] Focus chain N [auth A] Focus chain NA [auth J] Focus chain O [auth A] Focus chain OA [auth J] Focus chain PA [auth K] Focus chain Q [auth B] Focus chain QA [auth K] Focus chain R [auth B] Focus chain RA [auth L] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E 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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-05-29

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

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
Version 1.5: 2023-01-25
Changes: Database references, Derived calculations