2YWQ | pdb_00002ywq

Crystal structure of Thermus thermophilus Protein Y N-terminal domain

PDB DOI: https://doi.org/10.2210/pdb2YWQ/pdb

Classification: RIBOSOMAL PROTEIN
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-04-21 Released: 2008-04-15
Deposition Author(s): Kawazoe, M., Takemoto, C., Kaminishi, T., Tatsuguchi, A., Saito, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free:
0.294 (Depositor), 0.288 (DCC)
R-Value Work:
0.238 (Depositor), 0.237 (DCC)
R-Value Observed:
0.238 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2YWQ

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Thermus thermophilus Protein Y N-terminal domain

Kawazoe, M., Takemoto, C., Kaminishi, T., Tatsuguchi, A., Saito, Y., Shirouzu, M., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 49.02 kDa
Atom Count: 2,908
Modeled Residue Count: 357
Deposited Residue Count: 420
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal subunit interface protein	A, B, C, D	105	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: TTHA1294
UniProt
Find proteins for Q5SIS0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIS0 Go to UniProtKB: Q5SIS0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SIS0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE Query on MSE	A, B, C, D	MET	Selenomethionine	C₅ H₁₁ N O₂ Se

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.294 (Depositor), 0.288 (DCC)
R-Value Work: 0.238 (Depositor), 0.237 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.774	α = 90
b = 81.774	β = 90
c = 136.553	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-04-15

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-04-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary