1O5J | pdb_00001o5j

Crystal structure of Periplasmic divalent cation tolerance protein (TM1056) from Thermotoga maritima at 1.95 A resolution

PDB DOI: https://doi.org/10.2210/pdb1O5J/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2003-09-19 Released: 2003-09-30
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.221 (Depositor), 0.229 (DCC)
R-Value Work:
0.156 (Depositor), 0.167 (DCC)
R-Value Observed:
0.159 (Depositor)

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 Periplasmic divalent cation tolerance protein (TM1056) from Thermotoga maritima at 1.95 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 13.75 kDa
Atom Count: 964
Modeled Residue Count: 104
Deposited Residue Count: 113
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
periplasmic divalent cation tolerance protein	A	113	Thermotoga maritima	Mutation(s): 2 Gene Names: TM1056
UniProt
Find proteins for Q9X0E6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0E6 Go to UniProtKB: Q9X0E6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X0E6
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: 1.95 Å
R-Value Free: 0.221 (Depositor), 0.229 (DCC)
R-Value Work: 0.156 (Depositor), 0.167 (DCC)
R-Value Observed: 0.159 (Depositor)

Diffraction Data:

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.514	α = 90
b = 52.514	β = 90
c = 34.707	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
RESOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-09-30

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2003-09-30
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Version format compliance
Version 1.3: 2018-07-18
Changes: Data collection, Database references
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-11-06
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.