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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.217 (Depositor), 0.221 (DCC)
R-Value Work:
0.168 (Depositor), 0.171 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6MRF

This is version 1.1 of the entry. See complete history.

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.

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

Find similar proteins by:

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... 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	V5VCW7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.217 (Depositor), 0.221 (DCC)
R-Value Work: 0.168 (Depositor), 0.171 (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

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-10-31

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.