2PIM | pdb_00002pim

CRYSTAL STRUCTURE OF A PUTATIVE THIOESTERASE, PHENYLACETIC ACID DEGRADATION-RELATED PROTEIN (REUT_B4779) FROM RALSTONIA EUTROPHA JMP134 AT 2.20 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb2PIM/pdb

Classification: HYDROLASE
Organism(s): Cupriavidus pinatubonensis JMP134
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-04-13 Released: 2007-05-01
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.222 (Depositor), 0.220 (DCC)
R-Value Work:
0.182 (Depositor), 0.190 (DCC)
R-Value Observed:
0.185 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of Phenylacetic acid degradation-related protein (YP_298971.1) from Ralstonia eutropha JMP134 at 2.20 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 15 kDa
Atom Count: 1,031
Modeled Residue Count: 132
Deposited Residue Count: 141
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylacetic acid degradation-related protein	A	141	Cupriavidus pinatubonensis JMP134	Mutation(s): 0 Gene Names: YP_298971.1, Reut_B4779
UniProt
Find proteins for Q46RV7 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)) Explore Q46RV7 Go to UniProtKB: Q46RV7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q46RV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.222 (Depositor), 0.220 (DCC)
R-Value Work: 0.182 (Depositor), 0.190 (DCC)
R-Value Observed: 0.185 (Depositor)

Diffraction Data: https://doi.org/10.18430/M32PIM

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.774	α = 90
b = 111.774	β = 90
c = 46.461	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-05-01

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-05-01
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.