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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.239 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.230 (DCC) 

Literature

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

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 assigned by authors.

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein TM1410	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	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
UNL	EA [auth D], G [auth A], KA [auth E], O [auth B], PA [auth F], Z [auth C]	Unknown ligand PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	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), 0.250 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.230 (DCC) 

Diffraction Data: https://doi.org/10.18430/M32AAM

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

Entry History 

Deposition Data

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

Revision History  

• 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