2D4O | pdb_00002d4o

Crystal structure of TTHA1254 (I68M mutant) from Thermus thermophilus HB8

PDB DOI: https://doi.org/10.2210/pdb2D4O/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-10-21 Released: 2006-04-21
Deposition Author(s): Mizohata, E., Uchikubo, T., Kinoshita, Y., Terada, T., Shirouzu, M., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.236 (Depositor), 0.186 (DCC)
R-Value Work:
0.180 (Depositor), 0.191 (DCC)
R-Value Observed:
0.183 (Depositor)

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

Literature

Crystal structure of TTHA1254 (I68M mutant) from Thermus thermophilus HB8

Mizohata, E., Uchikubo, T., Kinoshita, Y., Terada, T., Shirouzu, M., Kuramitsu, S., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 15.64 kDa
Atom Count: 1,108
Modeled Residue Count: 130
Deposited Residue Count: 141
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein TTHA1254	A	141	Thermus thermophilus HB8	Mutation(s): 3
UniProt
Find proteins for Q72J89 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72J89 Go to UniProtKB: Q72J89
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72J89
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.236 (Depositor), 0.186 (DCC)
R-Value Work: 0.180 (Depositor), 0.191 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.463	α = 90
b = 58.463	β = 90
c = 77.679	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-04-21

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2006-04-21
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2024-10-16
Changes: Data collection, Structure summary

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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.