5L6Z

Crystal structure of D62A mutant of Thermotoga maritima TmPEP1050 aminopeptidase

• PDB DOI: https://doi.org/10.2210/pdb5L6Z/pdb

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


• Deposited: 2016-06-01 Released: 2017-06-21 
• Deposition Author(s): Dutoit, R., Van Elder, D., Bauvois, C.
• Funding Organization(s): Commission communautaire francaise

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.215 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

M42 aminopeptidase catalytic site: the structural and functional role of a strictly conserved aspartate residue

Dutoit, R., Brandt, N., Van Gompel, T., Van Elder, D., Van Dyck, J., Sobott, F., Droogmans, L.

(2020) Proteins 

• DOI: https://doi.org/10.1002/prot.25982

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 72.37 kDa 
• Atom Count: 5,798 
• Modelled Residue Count: 623 
• Deposited Residue Count: 662 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
leucylaminopeptidase	A, B	331	Thermotoga maritima MSB8	Mutation(s): 1  Gene Names: TM_1050, Tmari_1054 EC: 3.2.1.4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
NA	D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.215 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.18	α = 90
b = 113.96	β = 90
c = 267.23	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Dutoit, R., Van Elder, D., Bauvois, C.

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Funding Organization	Location	Grant Number
Commission communautaire francaise	Belgium	--

Revision History  

• Version 1.0: 2017-06-21
  Type: Initial release
  
• Version 2.0: 2021-02-24
  Changes: Atomic model, Database references
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description