3TB5 | pdb_00003tb5

Crystal Structure of the Enterococcus faecalis Methionine aminopeptidase apo form

PDB DOI: https://doi.org/10.2210/pdb3TB5/pdb

Classification: HYDROLASE
Organism(s): Enterococcus faecalis HIP11704
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-08-05 Released: 2012-08-08
Deposition Author(s): Kishor, C., Gumpena, R., Reddi, R., Addlagatta, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.255 (Depositor), 0.252 (DCC)
R-Value Work:
0.197 (Depositor)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Structural studies of Enterococcus faecalis methionine aminopeptidase and design of microbe specific 2,2'-bipyridine based inhibitors

Kishor, C., Gumpena, R., Reddi, R., Addlagatta, A.

(2012) Medchemcomm 3: 1406-1412

DOI: https://doi.org/10.1039/c2md20096a

Macromolecule Content

Total Structure Weight: 88.73 kDa
Atom Count: 5,897
Modeled Residue Count: 715
Deposited Residue Count: 792
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine aminopeptidase	A, B, C	264	Enterococcus faecalis HIP11704	Mutation(s): 0 Gene Names: EFHG_00941, MetAP EC: 3.4.11.18

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.255 (Depositor), 0.252 (DCC)
R-Value Work: 0.197 (Depositor)
R-Value Observed: 0.200 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.74	α = 90
b = 132.13	β = 133.36
c = 85.3	γ = 90

Software Package:

Software Name	Purpose
APEX	data collection
MOLREP	phasing
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-08-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-08
Type: Initial release
Version 1.1: 2013-06-26
Changes: Database references
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.