2AAM | pdb_00002aam

Crystal structure of a putative glycosidase (tm1410) from thermotoga maritima at 2.20 A resolution

PDB DOI: https://doi.org/10.2210/pdb2AAM/pdb

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

Deposited: 2005-07-13 Released: 2005-07-26
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.239 (Depositor), 0.245 (DCC)
R-Value Work:
0.216 (Depositor), 0.226 (DCC)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of hypothetical protein (tm1410) from THERMOTOGA MARITIMA at 2.20 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 222.89 kDa
Atom Count: 15,499
Modeled Residue Count: 1,717
Deposited Residue Count: 1,854
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein TM1410	A, B, C, D, E A, B, C, D, E, F	309	Thermotoga maritima	Mutation(s): 6 Gene Names: tm1410
UniProt
Find proteins for Q9X1D0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1D0 Go to UniProtKB: Q9X1D0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X1D0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain WA [auth F] SDF format, chain W [auth B] SDF format, chain VA [auth F] SDF format, chain V [auth B] SDF format, chain UA [auth F] SDF format, chain U [auth B] SDF format, chain TA [auth F] SDF format, chain T [auth B] SDF format, chain SA [auth F] SDF format, chain S [auth B] SDF format, chain RA [auth F] SDF format, chain R [auth B] SDF format, chain QA [auth F] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain OA [auth E] SDF format, chain NA [auth E] SDF format, chain N [auth A] SDF format, chain MA [auth E] SDF format, chain M [auth A] SDF format, chain LA [auth E] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain JA [auth D] SDF format, chain J [auth A] SDF format, chain IA [auth D] SDF format, chain I [auth A] SDF format, chain HA [auth D] SDF format, chain H [auth A] SDF format, chain GA [auth D] SDF format, chain FA [auth D] SDF format, chain DA [auth C] SDF format, chain CA [auth C] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain WA [auth F] MOL2 format, chain W [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain WA [auth F] mmCIF format, chain W [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth E] mmCIF format, chain NA [auth E] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] FA [auth D] AA [auth C], BA [auth C], CA [auth C], DA [auth C], FA [auth D], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], L [auth A], LA [auth E], M [auth A], MA [auth E], N [auth A], NA [auth E], OA [auth E], P [auth B], Q [auth B], QA [auth F], R [auth B], RA [auth F], S [auth B], SA [auth F], T [auth B], TA [auth F], U [auth B], UA [auth F], V [auth B], VA [auth F], W [auth B], WA [auth F], X [auth B], Y [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain VA [auth F] Focus chain W [auth B] Focus chain WA [auth F] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain VA [auth F] Focus chain W [auth B] Focus chain WA [auth F] Focus chain X [auth B] Focus chain Y [auth B]
UNL Query on UNL Download:Ideal Coordinates CCD File	EA [auth D] G [auth A] KA [auth E] O [auth B] PA [auth F] EA [auth D], G [auth A], KA [auth E], O [auth B], PA [auth F], Z [auth C]	Unknown ligand PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain G [auth A] Focus chain KA [auth E] Focus chain O [auth B] Focus chain PA [auth F] Focus chain Z [auth C] Interactions & Density Focus chain EA [auth D] Focus chain G [auth A] Focus chain KA [auth E] Focus chain O [auth B] Focus chain PA [auth F] Focus chain Z [auth C]

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	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: 0.239 (Depositor), 0.245 (DCC)
R-Value Work: 0.216 (Depositor), 0.226 (DCC)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 194.93	α = 90
b = 84.62	β = 119.9
c = 195.01	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELX	phasing
SHARP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-07-26

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2005-07-26
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2023-01-25
Changes: Database references, Derived calculations
Version 1.4: 2024-11-20
Changes: Data collection, Refinement description, Structure summary