2YWA | pdb_00002ywa

Crystal structure of uncharacterized conserved protein from Thermus thermophilus HB8

PDB DOI: https://doi.org/10.2210/pdb2YWA/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-04-20 Released: 2007-10-23
Deposition Author(s): Kitamura, Y., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.243 (Depositor), 0.255 (DCC)
R-Value Work:
0.216 (Depositor), 0.227 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of uncharacterized conserved protein from Thermus thermophilus HB8

Kitamura, Y., Yokoyama, S., Kuramitsu, S.

To be published.

Macromolecule Content

Total Structure Weight: 56.18 kDa
Atom Count: 3,815
Modeled Residue Count: 459
Deposited Residue Count: 476
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein TTHA0048	A, B, C, D	119	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SM95 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SM95 Go to UniProtKB: Q5SM95
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SM95
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.243 (Depositor), 0.255 (DCC)
R-Value Work: 0.216 (Depositor), 0.227 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.76	α = 90
b = 121.76	β = 90
c = 322.56	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-10-23

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-10-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-10-11
Changes: Refinement description
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-11-15
Changes: Data collection
Version 1.5: 2024-10-16
Changes: 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.