1NC7 | pdb_00001nc7

Crystal Structure of Thermotoga maritima 1070

PDB DOI: https://doi.org/10.2210/pdb1NC7/pdb

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

Deposited: 2002-12-04 Released: 2003-07-01
Deposition Author(s): Kim, Y., Joachimiak, A., Edwards, A., Skarina, T., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.190 (Depositor), 0.189 (DCC)
R-Value Work:
0.170 (Depositor), 0.170 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure Analysis of Thermotoga maritima Hypothetical protein TM1070

Kim, Y., Joachimiak, A., Edwards, A., Skarina, T., Savchenko, A.

To be published.

Macromolecule Content

Total Structure Weight: 65.02 kDa
Atom Count: 4,302
Modeled Residue Count: 465
Deposited Residue Count: 552
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein TM1070	A, B, C, D	138	Thermotoga maritima	Mutation(s): 6 Gene Names: TM1070
UniProt
Find proteins for Q9X0F9 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0F9 Go to UniProtKB: Q9X0F9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X0F9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain O [auth D] SDF format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain O [auth D] MOL2 format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain O [auth D] mmCIF format, chain L [auth B]	J [auth A], L [auth B], O [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain O [auth D] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain O [auth D]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain K [auth A] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain K [auth A] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain K [auth A]	K [auth A], M [auth C], P [auth D], Q [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain K [auth A] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain N [auth D]	E [auth A], N [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain N [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	F [auth A], G [auth A], H [auth A], I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

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: 1.55 Å
R-Value Free: 0.190 (Depositor), 0.189 (DCC)
R-Value Work: 0.170 (Depositor), 0.170 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.435	α = 63.18
b = 54.453	β = 62.27
c = 55.178	γ = 89.81

Software Package:

Software Name	Purpose
d*TREK	data scaling
HKL-2000	data reduction
CNS	refinement
d*TREK	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2003-07-01

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2003-07-01
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary