3WHP | pdb_00003whp

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 (Depositor), 0.279 (DCC)
R-Value Work:
0.224 (Depositor), 0.233 (DCC)
R-Value Observed:
0.224 (Depositor)

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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
Modeled Residue Count: 192
Deposited Residue Count: 290
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.279 (DCC)
R-Value Work: 0.224 (Depositor), 0.233 (DCC)
R-Value Observed: 0.224 (Depositor)

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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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

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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.