2F4P | pdb_00002f4p

Crystal structure of a cupin-like protein (tm1010) from thermotoga maritima msb8 at 1.90 A resolution

PDB DOI: https://doi.org/10.2210/pdb2F4P/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-11-23 Released: 2006-01-24
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.216 (Depositor), 0.225 (DCC)
R-Value Work:
0.160 (Depositor), 0.174 (DCC)
R-Value Observed:
0.164 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of hypothetical protein (tm1010) from THERMOTOGA MARITIMA at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 67.32 kDa
Atom Count: 4,826
Modeled Residue Count: 532
Deposited Residue Count: 588
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein TM1010	A, B, C, D	147	Thermotoga maritima MSB8	Mutation(s): 2 Gene Names: tm1010
UniProt
Find proteins for Q9X0A3 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0A3 Go to UniProtKB: Q9X0A3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X0A3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D]	F [auth A] G [auth A] I [auth B] J [auth B] K [auth B] F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B], N [auth C], O [auth C], Q [auth D], R [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D]
UNL Query on UNL Download:Ideal Coordinates CCD File	E [auth A], H [auth B], M [auth C], P [auth D]	Unknown ligand LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain P [auth D]

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: 1.90 Å
R-Value Free: 0.216 (Depositor), 0.225 (DCC)
R-Value Work: 0.160 (Depositor), 0.174 (DCC)
R-Value Observed: 0.164 (Depositor)

Diffraction Data:

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.746	α = 90
b = 71.746	β = 90
c = 188.6	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-01-24

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2006-01-24
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2023-01-25
Changes: Database references, Derived calculations
Version 1.4: 2024-11-06
Changes: Data collection, Structure summary

2F4P | pdb_00002f4p

Crystal structure of a cupin-like protein (tm1010) from thermotoga maritima msb8 at 1.90 A resolution

Literature

Crystal structure of hypothetical protein (tm1010) from THERMOTOGA MARITIMA at 1.90 A resolution

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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