2PJU | pdb_00002pju

Crystal structure of propionate catabolism operon regulatory protein prpR

PDB DOI: https://doi.org/10.2210/pdb2PJU/pdb

Classification: TRANSCRIPTION
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-04-16 Released: 2007-05-22
Deposition Author(s): Ramagopal, U.A., Toro, R., Gilmore, M., Wu, B., Koss, J., Groshong, C., Gheyi, T., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.252 (Depositor), 0.270 (DCC)
R-Value Work:
0.201 (Depositor), 0.229 (DCC)
R-Value Observed:
0.204 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2PJU

This is version 1.7 of the entry. See complete history.

Literature

Crystal structure of propionate catabolism operon regulatory protein prpR

Ramagopal, U.A., Toro, R., Gilmore, M., Wu, B., Koss, J., Groshong, C., Gheyi, T., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 100.31 kDa
Atom Count: 6,218
Modeled Residue Count: 766
Deposited Residue Count: 900
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Propionate catabolism operon regulatory protein	A, B, C, D	225	Escherichia coli	Mutation(s): 1 Gene Names: prpR, b0330, JW0322
UniProt
Find proteins for P77743 (Escherichia coli (strain K12)) Explore P77743 Go to UniProtKB: P77743
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P77743
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.252 (Depositor), 0.270 (DCC)
R-Value Work: 0.201 (Depositor), 0.229 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.657	α = 85.03
b = 58.545	β = 88.56
c = 103.576	γ = 86.94

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
HKL2Map	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-05-22

Deposition Author(s):

Ramagopal, U.A.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-05-22
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-11-14
Changes: Data collection, Structure summary
Version 1.5: 2021-02-03
Changes: Database references, Structure summary
Version 1.6: 2021-10-20
Changes: Database references
Version 1.7: 2024-02-21
Changes: Data collection

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.