3LOC | pdb_00003loc

Crystal structure of putative transcriptional regulator ycdc

PDB DOI: https://doi.org/10.2210/pdb3LOC/pdb
Entry: 3LOC supersedes: 1PB6

Classification: TRANSCRIPTION
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-02-03 Released: 2010-03-16
Deposition Author(s): Patskovsky, Y.V., Knapik, A.A., Mennella, V., Burley, S.K., Minor, W., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.229 (Depositor)
R-Value Work:
0.195 (Depositor), 0.211 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3LOC

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

Literature

Crystal Structure of Hypothetical Transcriptional Regulator Ycdc from Escherichia Coli

Patskovsky, Y.V., Mennella, V., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 96.25 kDa
Atom Count: 6,366
Modeled Residue Count: 803
Deposited Residue Count: 848
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator rutR	A, B, C, D	212	Escherichia coli K-12	Mutation(s): 0 Gene Names: b1013, JW0998, rutR, ycdC
UniProt
Find proteins for P0ACU2 (Escherichia coli (strain K12)) Explore P0ACU2 Go to UniProtKB: P0ACU2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ACU2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
URA Query on URA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	URACIL C₄ H₄ N₂ O₂ ISAKRJDGNUQOIC-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

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: 2.50 Å
R-Value Free: 0.229 (Depositor)
R-Value Work: 0.195 (Depositor), 0.211 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.02	α = 90
b = 139.61	β = 90
c = 156	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SOLVE	phasing
RESOLVE	model building
HKL-3000	phasing
REFMAC	refinement
Coot	model building
DENZO	data reduction
SCALEPACK	data scaling
RESOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-03-16

Deposition Author(s):

Patskovsky, Y.V.

New York SGX Research Center for Structural Genomics (NYSGXRC)

This entry supersedes: 1PB6

Revision History (Full details and data files)

Version 1.0: 2010-03-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2021-02-10
Changes: Derived calculations, Structure summary
Version 1.4: 2022-04-13
Changes: Database references, Structure summary
Version 1.5: 2024-10-16
Changes: Data collection, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.