2Q78 | pdb_00002q78

Crystal structure of a thioesterase-like protein (tm0581) from thermotoga maritima msb8 at 2.20 A resolution

PDB DOI: https://doi.org/10.2210/pdb2Q78/pdb

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

Deposited: 2007-06-06 Released: 2007-06-19
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.224 (Depositor), 0.270 (DCC)
R-Value Work:
0.175 (Depositor), 0.230 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.7 of the entry. See complete history.

Literature

Crystal structure of Uncharacterized protein TM0581 (TM0581) from Thermotoga maritima at 2.20 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 147.97 kDa
Atom Count: 9,110
Modeled Residue Count: 1,056
Deposited Residue Count: 1,224
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D, E A, B, C, D, E, F, G, H	153	Thermotoga maritima MSB8	Mutation(s): 5 Gene Names: TM_0581
UniProt
Find proteins for Q9WZ50 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZ50 Go to UniProtKB: Q9WZ50
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WZ50
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLC Query on MLC Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain M [auth D] SDF format, chain N [auth E] SDF format, chain Q [auth G] SDF format, chain R [auth H] SDF format, chain P [auth F] SDF format, chain K [auth C] SDF format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth D] MOL2 format, chain N [auth E] MOL2 format, chain Q [auth G] MOL2 format, chain R [auth H] MOL2 format, chain P [auth F] MOL2 format, chain K [auth C] MOL2 format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth D] mmCIF format, chain N [auth E] mmCIF format, chain Q [auth G] mmCIF format, chain R [auth H] mmCIF format, chain P [auth F] mmCIF format, chain K [auth C] mmCIF format, chain I [auth A]	I [auth A] J [auth B] K [auth C] M [auth D] N [auth E] I [auth A], J [auth B], K [auth C], M [auth D], N [auth E], P [auth F], Q [auth G], R [auth H]	MALONYL-COENZYME A C₂₄ H₃₈ N₇ O₁₉ P₃ S LTYOQGRJFJAKNA-DVVLENMVSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain O [auth F] MOL2 format, chain L [auth D] MOL2 format, chain O [auth F] mmCIF format, chain L [auth D] mmCIF format, chain O [auth F]	L [auth D], O [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth D] Focus chain O [auth F] Interactions & Density Focus chain L [auth D] Focus chain O [auth F]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.224 (Depositor), 0.270 (DCC)
R-Value Work: 0.175 (Depositor), 0.230 (DCC)
R-Value Observed: 0.177 (Depositor)

Diffraction Data: https://doi.org/10.18430/M32Q78

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.347	α = 90
b = 90.706	β = 90
c = 230.42	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-06-19

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-06-19
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2017-10-25
Changes: Author supporting evidence
Version 1.5: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.6: 2023-01-25
Changes: Database references, Derived calculations
Version 1.7: 2024-10-16
Changes: Data collection, Refinement description, Structure summary