5YTQ | pdb_00005ytq

Crystal Structure of TTHA0139 L34A with Lanthanum from Thermus thermophilus HB8

PDB DOI: https://doi.org/10.2210/pdb5YTQ/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-11-19 Released: 2018-11-21
Deposition Author(s): Takao, K., Inoue, M., Fukui, K., Yano, T., Masui, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.274 (Depositor), 0.274 (DCC)
R-Value Work:
0.263 (Depositor), 0.264 (DCC)
R-Value Observed:
0.264 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5YTQ

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

Literature

Crystal Structure of TTHA0139 L34A with Lanthanum from Thermus thermophilus HB8

Takao, K., Inoue, M., Fukui, K., Yano, T., Masui, R.

To be published.

Macromolecule Content

Total Structure Weight: 26.68 kDa
Atom Count: 1,586
Modeled Residue Count: 203
Deposited Residue Count: 231
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TTHA0139	A, B, C	77	Thermus thermophilus HB8	Mutation(s): 1 Gene Names: TTHA0139
UniProt
Find proteins for Q5SM04 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SM04 Go to UniProtKB: Q5SM04
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SM04
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LA Query on LA Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain H [auth C] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain H [auth C] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth B], G [auth C], H [auth C]	LANTHANUM (III) ION La CZMAIROVPAYCMU-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.274 (Depositor), 0.274 (DCC)
R-Value Work: 0.263 (Depositor), 0.264 (DCC)
R-Value Observed: 0.264 (Depositor)

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.224	α = 90
b = 50.224	β = 90
c = 174.648	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-11-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-11-21
Type: Initial release
Version 1.1: 2024-03-27
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.