2GLF | pdb_00002glf

Crystal structure of Aminipeptidase (M18 family) from Thermotoga Maritima

• PDB DOI: https://doi.org/10.2210/pdb2GLF/pdb

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


• Deposited: 2006-04-04 Released: 2006-06-13 
• Deposition Author(s): Min, T., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.239 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Crystal structure of Aminipeptidase (M18 family) from Thermotoga Maritima

Min, T., Shapiro, L.

To be published.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 204.16 kDa 
• Atom Count: 14,643 
• Modeled Residue Count: 1,800 
• Deposited Residue Count: 1,800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable M18-family aminopeptidase 1	A, B, C, D	450	Thermotoga maritima	Mutation(s): 13  Gene Names: apeA EC: 3.4.11
UniProt
Find proteins for Q9WYJ9 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYJ9  Go to UniProtKB:  Q9WYJ9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.239 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 191.225	α = 90
b = 191.225	β = 90
c = 191.225	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-13 
Deposition Author(s): Min, T., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-06-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Structure summary