4FO8 | pdb_00004fo8

Pseudomonas aeruginosa MetAP with Met, in Mn form

PDB DOI: https://doi.org/10.2210/pdb4FO8/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-06-20 Released: 2013-07-03
Deposition Author(s): Ye, Q.Z., Lu, J.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.157 (Depositor), 0.160 (DCC)
R-Value Observed:
0.159 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Methionine excision captured by the structures of a methionine aminopeptidase

Lu, J.P., Ye, Q.Z.

To be published.

Macromolecule Content

Total Structure Weight: 126.86 kDa
Atom Count: 9,002
Modelled Residue Count: 1,045
Deposited Residue Count: 1,120
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine aminopeptidase	A, B, C, D	280	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: map, PA3657 EC: 3.4.11.18
UniProt
Find proteins for Q9HXY1 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HXY1 Go to UniProtKB: Q9HXY1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HXY1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MET Query on MET Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D]	I [auth A], M [auth B], Q [auth C], U [auth D]	METHIONINE C₅ H₁₁ N O₂ S FFEARJCKVFRZRR-BYPYZUCNSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D]	E [auth A] F [auth A] G [auth A] H [auth A] J [auth B] E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], N [auth C], O [auth C], P [auth C], R [auth D], S [auth D], T [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.200 (Depositor), 0.200 (DCC)
R-Value Work: 0.157 (Depositor), 0.160 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.651	α = 90
b = 105.664	β = 90
c = 133.155	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-07-03

Deposition Author(s):

Ye, Q.Z.

Lu, J.P.

Revision History (Full details and data files)

Version 1.0: 2013-07-03
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations