3IJ3 | pdb_00003ij3

1.8 Angstrom Resolution Crystal Structure of Cytosol Aminopeptidase from Coxiella burnetii

PDB DOI: https://doi.org/10.2210/pdb3IJ3/pdb

Classification: HYDROLASE
Organism(s): Coxiella burnetii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-08-03 Released: 2009-08-11
Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.177 (Depositor), 0.191 (DCC)
R-Value Work:
0.147 (Depositor), 0.159 (DCC)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

1.8 Angstrom Resolution Crystal Structure of Cytosol Aminopeptidase from Coxiella burnetii

Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 55.39 kDa
Atom Count: 4,358
Modeled Residue Count: 457
Deposited Residue Count: 482
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosol aminopeptidase	A	482	Coxiella burnetii	Mutation(s): 0 Gene Names: CBU_0572, pepB EC: 3.4.11.1
UniProt
Find proteins for Q83DX0 (Coxiella burnetii (strain RSA 493 / Nine Mile phase I)) Explore Q83DX0 Go to UniProtKB: Q83DX0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q83DX0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain O [auth A]	O [auth A], P [auth A], Q [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A]	M [auth A], N [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain M [auth A] Focus chain N [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
LI Query on LI Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	LITHIUM ION Li HBBGRARXTFLTSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.177 (Depositor), 0.191 (DCC)
R-Value Work: 0.147 (Depositor), 0.159 (DCC)
R-Value Observed: 0.149 (Depositor)

Diffraction Data:

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.803	α = 90
b = 112.803	β = 90
c = 78.089	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-08-11

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-08-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description