3EOQ | pdb_00003eoq

The crystal structure of putative zinc protease beta-subunit from Thermus thermophilus HB8

PDB DOI: https://doi.org/10.2210/pdb3EOQ/pdb

Classification: HYDROLASE
Organism(s): Thermus thermophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-09-29 Released: 2009-03-17
Deposition Author(s): Ohtsuka, J., Ichihara, Y., Ebihara, A., Yokoyama, S., Kuramitsu, S., Nagata, K., Tanokura, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.237 (Depositor), 0.237 (DCC)
R-Value Work:
0.187 (Depositor), 0.187 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3EOQ

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

Literature

Crystal structure of TTHA1264, a putative M16-family zinc peptidase from Thermus thermophilus HB8 that is homologous to the beta subunit of mitochondrial processing peptidase.

Ohtsuka, J., Ichihara, Y., Ebihara, A., Nagata, K., Tanokura, M.

(2009) Proteins

PubMed: 19241474 Search on PubMed
DOI: https://doi.org/10.1002/prot.22365
Primary Citation Related Structures:
3EOQ

Organizational Affiliation

Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.

Macromolecule Content

Total Structure Weight: 92.12 kDa
Atom Count: 6,739
Modeled Residue Count: 811
Deposited Residue Count: 812
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative zinc protease	A, B	406	Thermus thermophilus	Mutation(s): 0 Gene Names: TTHA1264 EC: 3.4.24.56
UniProt
Find proteins for Q5SIV0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIV0 Go to UniProtKB: Q5SIV0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SIV0
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.237 (Depositor), 0.237 (DCC)
R-Value Work: 0.187 (Depositor), 0.187 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.34	α = 90
b = 94.202	β = 90
c = 134.454	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-03-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-03-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-09
Changes: Data collection, Database references, Derived calculations, 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.