5TPM | pdb_00005tpm

2.8 Angstrom Crystal Structure of the C-terminal Dimerization Domain of Transcriptional Regulator PdhR from Escherichia coli.

PDB DOI: https://doi.org/10.2210/pdb5TPM/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli CFT073
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-10-20 Released: 2016-11-02
Deposition Author(s): Minasov, G., Wawrzak, Z., Sandoval, J., Skarina, T., Grimshaw, S., Kwon, K., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.257 (Depositor), 0.258 (DCC)
R-Value Work:
0.222 (Depositor), 0.235 (DCC)
R-Value Observed:
0.224 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

2.8 Angstrom Crystal Structure of the C-terminal Dimerization Domain of Transcriptional Regulator PdhR from Escherichia coli.

Minasov, G., Wawrzak, Z., Sandoval, J., Skarina, T., Grimshaw, S., Kwon, K., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 74.85 kDa
Atom Count: 4,818
Modeled Residue Count: 588
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate dehydrogenase complex repressor	A, B, C, D	159	Escherichia coli CFT073	Mutation(s): 0 Gene Names: pdhR, c0140
UniProt
Find proteins for P0ACL9 (Escherichia coli (strain K12)) Explore P0ACL9 Go to UniProtKB: P0ACL9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ACL9
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.257 (Depositor), 0.258 (DCC)
R-Value Work: 0.222 (Depositor), 0.235 (DCC)
R-Value Observed: 0.224 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.397	α = 90
b = 95.347	β = 114.09
c = 70.001	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-11-02

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-11-02
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.