8QA8

Crystal structure of the C-terminally truncated transcriptional repressor protein KorB from the RK2 plasmid complexed with CTP-gamma-S

PDB DOI: https://doi.org/10.2210/pdb8QA8/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-08-22 Released: 2024-02-21
Deposition Author(s): McLean, T.C., Mundy, J.E.A., Lawson, D.M., Le, T.B.K.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Wellcome Trust, Royal Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.256
R-Value Work: 0.227
R-Value Observed: 0.229

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the C-terminally truncated transcriptional repressor protein KorB from the RK2 plasmid complexed with CTP-gamma-S

McLean, T.C., Mundy, J.E.A., Lawson, D.M., Le, T.B.K.

To be published.

Macromolecule Content

Total Structure Weight: 162.19 kDa
Atom Count: 9,992
Modelled Residue Count: 1,201
Deposited Residue Count: 1,422
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional repressor protein KorB	A, B, C, D, E A, B, C, D, E, F	237	Escherichia coli	Mutation(s): 0 Gene Names: korB
UniProt
Find proteins for P07674 (Escherichia coli) Explore P07674 Go to UniProtKB: P07674
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07674
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CTP (Subject of Investigation/LOI) Query on CTP Download Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain Z [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain Z [auth E]	EA [auth F] G [auth A] L [auth B] Q [auth C] U [auth D] EA [auth F], G [auth A], L [auth B], Q [auth C], U [auth D], Z [auth E]	CYTIDINE-5'-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₄ P₃ PCDQPRRSZKQHHS-XVFCMESISA-N		Interactions Focus chain EA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain Z [auth E] Interactions & Density Focus chain EA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain Z [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain H [auth A] SDF format, chain HA [auth F] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D]	AA [auth E] BA [auth E] CA [auth E] DA [auth E] FA [auth F] AA [auth E], BA [auth E], CA [auth E], DA [auth E], FA [auth F], GA [auth F], H [auth A], HA [auth F], I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], O [auth B], P [auth B], R [auth C], S [auth C], T [auth C], V [auth D], W [auth D], X [auth D], Y [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain H [auth A] Focus chain HA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain H [auth A] Focus chain HA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.256
R-Value Work: 0.227
R-Value Observed: 0.229
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.686	α = 90
b = 152.71	β = 90
c = 198.274	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-02-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/X01097X/1
Wellcome Trust	United Kingdom	221776/Z/20/Z
Royal Society	United Kingdom	URF/R/201020