3PEI | pdb_00003pei

Crystal Structure of Cytosol Aminopeptidase from Francisella tularensis

PDB DOI: https://doi.org/10.2210/pdb3PEI/pdb

Classification: HYDROLASE
Organism(s): Francisella tularensis subsp. tularensis SCHU S4
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2010-10-26 Released: 2010-12-01
Deposition Author(s): Maltseva, N., Kim, Y., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.210 (Depositor), 0.206 (DCC)
R-Value Work:
0.165 (Depositor), 0.161 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Cytosol Aminopeptidase from Francisella tularensis

Maltseva, N., Kim, Y., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 55.31 kDa
Atom Count: 4,014
Modeled Residue Count: 456
Deposited Residue Count: 486
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosol aminopeptidase	A	486	Francisella tularensis subsp. tularensis SCHU S4	Mutation(s): 0 Gene Names: FTT_1318c, pepA EC: 3.4.11.1 (PDB Primary Data), 3.4.11.10 (UniProt)
UniProt
Find proteins for Q5NFC1 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NFC1 Go to UniProtKB: Q5NFC1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5NFC1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain D [auth A] MOL2 format, chain S [auth A] MOL2 format, chain D [auth A] mmCIF format, chain S [auth A] mmCIF format, chain D [auth A]	D [auth A], S [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain S [auth A] Interactions & Density Focus chain D [auth A] Focus chain S [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain X [auth A] MOL2 format, chain X [auth A] mmCIF format, chain X [auth A]	X [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain X [auth A] Interactions & Density Focus chain X [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A] E [auth A] M [auth A] N [auth A] O [auth A] C [auth A], E [auth A], M [auth A], N [auth A], O [auth A], Q [auth A], R [auth A], U [auth A], V [auth A], W [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain T [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain T [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A], T [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain G [auth A] SDF format, chain B [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain B [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain B [auth A]	B [auth A], G [auth A], I [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain G [auth A] Focus chain I [auth A] Interactions & Density Focus chain B [auth A] Focus chain G [auth A] Focus chain I [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Y [auth A] SDF format, chain P [auth A] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain F [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain P [auth A] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain P [auth A] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A]	F [auth A], H [auth A], J [auth A], P [auth A], Y [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain P [auth A] Focus chain Y [auth A] Interactions & Density Focus chain F [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain P [auth A] Focus chain Y [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.210 (Depositor), 0.206 (DCC)
R-Value Work: 0.165 (Depositor), 0.161 (DCC)
R-Value Observed: 0.167 (Depositor)

Diffraction Data:

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.483	α = 90
b = 161.483	β = 90
c = 105.27	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELX	model building
RESOLVE	model building
BUCCANEER	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
RESOLVE	phasing
BUCCANEER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-12-01

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-12-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Advisory, Refinement description
Version 1.3: 2024-11-27
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary