1YSP | pdb_00001ysp

Crystal structure of the C-terminal domain of E. coli transcriptional regulator KdgR.

PDB DOI: https://doi.org/10.2210/pdb1YSP/pdb

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

Deposited: 2005-02-08 Released: 2005-03-22
Deposition Author(s): Bochkarev, A., Lunin, V.V., Ezersky, A., Evdokimova, E., Skarina, T., Xu, X., Borek, D., Joachimiak, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.259 (Depositor), 0.254 (DCC)
R-Value Work:
0.212 (Depositor), 0.207 (DCC)
R-Value Observed:
0.214 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1YSP

This is version 1.4 of the entry. See complete history.

Literature

Structural study of effector binding specificity in IclR transcriptional regulators

Bochkarev, A., Lunin, V.V., Ezersky, A., Evdokimova, E., Skarina, T., Xu, X., Borek, D., Savchenko, A.

To be published.

Macromolecule Content

Total Structure Weight: 20.94 kDa
Atom Count: 1,535
Modeled Residue Count: 164
Deposited Residue Count: 181
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator kdgR	A	181	Escherichia coli	Mutation(s): 0 Gene Names: kdgR
UniProt
Find proteins for P76268 (Escherichia coli (strain K12)) Explore P76268 Go to UniProtKB: P76268
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P76268
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.259 (Depositor), 0.254 (DCC)
R-Value Work: 0.212 (Depositor), 0.207 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.54	α = 90
b = 31.54	β = 92.7
c = 37.05	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-03-22

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2005-03-22
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2011-10-05
Changes: Structure summary
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Derived calculations

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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.