6MRF | pdb_00006mrf

Crystal structure of a Methionine aminopeptidase MetAP from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb6MRF/pdb

• Classification: HYDROLASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-12 Released: 2018-10-31 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a Methionine aminopeptidase MetAP from Acinetobacter baumannii

Edwards, T.E., Mayclin, S.J., Lorimer, D.D., Horanyi, P.S., Seattle Structural Genomics Center for Infectious Disease

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30.04 kDa 
• Atom Count: 2,075 
• Modeled Residue Count: 247 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine aminopeptidase	A	270	Acinetobacter baumannii	Mutation(s): 0  Gene Names:  map_1, map, map1, map_2, A7M79_08180, A7M90_04815, A7N09_12540, ABUW_1234, APD06_11055, AZE33_14285, B4R90_02870, B9X91_03550, B9X95_11705, BGC29_02575, BWP00_06705, C2U32_08280, C7G90_05480, CBE85_00465, CBI29_02666, CEJ63_06330, CHQ89_03925, CPI82_15740, DCD76_03690, DCD77_06610, IX87_07995, LV38_03303, NCTC13421_01191 EC: 3.4.11.18
UniProt
Find proteins for V5VCW7 (Acinetobacter baumannii) Explore V5VCW7  Go to UniProtKB:  V5VCW7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.77	α = 90
b = 53.69	β = 90
c = 84.27	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-31 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-10-31
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description