3WHP

Crystal structure of the C-terminal domain of Themus thermophilus LitR in complex with cobalamin

PDB DOI: https://doi.org/10.2210/pdb3WHP/pdb

Classification: GENE REGULATION
Organism(s): Thermus thermophilus HB27
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-08-30 Released: 2014-09-03
Deposition Author(s): Agari, Y., Takano, H., Beppu, T., Ueda, K., Shinkai, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free: 0.247
R-Value Work: 0.224
R-Value Observed: 0.224

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the C-terminal domain of Themus thermophilus LitR in complex with cobalamin

Agari, Y., Takano, H., Beppu, T., Ueda, K., Shinkai, A.

To be published.

Macromolecule Content

Total Structure Weight: 32.89 kDa
Atom Count: 1,564
Modelled Residue Count: 192
Deposited Residue Count: 290
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable transcriptional regulator	A	290	Thermus thermophilus HB27	Mutation(s): 0 Gene Names: litR, TT_P0056
UniProt
Find proteins for Q746J7 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q746J7 Go to UniProtKB: Q746J7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q746J7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B12 Query on B12 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	COBALAMIN C₆₂ H₈₉ Co N₁₃ O₁₄ P LKVIQTCSMMVGFU-DWSMJLPVSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free: 0.247
R-Value Work: 0.224
R-Value Observed: 0.224
Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.366	α = 90
b = 95.366	β = 90
c = 50.333	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-09-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-03
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.