Macromolecule Content

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

3IJ3

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
R-Value Work: 0.147
R-Value Observed: 0.149

wwPDB Validation 3D Report Full Report

This is version 1.2 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.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q83DX0
Protein Feature View 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 O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A]	O [auth A], P [auth A], Q [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Ligand Interaction
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A]	M [auth A], N [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Ligand Interaction
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A]	I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction
LI Query on LI Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	LITHIUM ION Li HBBGRARXTFLTSG-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.177
R-Value Work: 0.147
R-Value Observed: 0.149
Space Group: P 3 2 1
Diffraction Data: https://doi.org/10.18430/M33IJ3

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

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.