3DCL

Crystal structure of TM1086

PDB DOI: https://doi.org/10.2210/pdb3DCL/pdb

Classification: structural genomics, unknown function
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-06-03 Released: 2008-08-05
Deposition Author(s): Chruszcz, M., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.212
R-Value Work: 0.164
R-Value Observed: 0.166

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of TM1086

Chruszcz, M., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 155.93 kDa
Atom Count: 11,271
Modelled Residue Count: 1,408
Deposited Residue Count: 1,420
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TM1086	A, B, C, D, E	284	Thermotoga maritima	Mutation(s): 0 Gene Names: TM_1086
UniProt
Find proteins for Q9X0H2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0H2 Go to UniProtKB: Q9X0H2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9X0H2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain F [auth A] SDF format, chain FA [auth E] SDF format, chain G [auth A] SDF format, chain GA [auth E] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth D]	AA [auth D] BA [auth D] F [auth A] FA [auth E] G [auth A] AA [auth D], BA [auth D], F [auth A], FA [auth E], G [auth A], GA [auth E], H [auth A], M [auth B], N [auth B], O [auth B], P [auth B], T [auth C], U [auth C], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain F [auth A] Focus chain FA [auth E] Focus chain G [auth A] Focus chain GA [auth E] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain F [auth A] Focus chain FA [auth E] Focus chain G [auth A] Focus chain GA [auth E] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain Z [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain JA [auth E] SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain Y [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain JA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B] mmCIF format, chain Y [auth C]	EA [auth D], JA [auth E], L [auth A], S [auth B], Y [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain JA [auth E] Focus chain L [auth A] Focus chain S [auth B] Focus chain Y [auth C] Interactions & Density Focus chain EA [auth D] Focus chain JA [auth E] Focus chain L [auth A] Focus chain S [auth B] Focus chain Y [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain HA [auth E] SDF format, chain I [auth A] SDF format, chain IA [auth E] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	CA [auth D] DA [auth D] HA [auth E] I [auth A] IA [auth E] CA [auth D], DA [auth D], HA [auth E], I [auth A], IA [auth E], J [auth A], K [auth A], Q [auth B], R [auth B], V [auth C], W [auth C], X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.212
R-Value Work: 0.164
R-Value Observed: 0.166
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.578	α = 90
b = 164.578	β = 90
c = 97.815	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
ARP	model building
Coot	model building
REFMAC	refinement
HKL-3000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
DM	phasing
RESOLVE	phasing
MAIN	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-08-05

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-08-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2011-10-05
Changes: Structure summary
Version 1.3: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-10-30
Changes: Data collection, Structure summary