3L92 | pdb_00003l92

Phosphopantetheine adenylyltransferase from Yersinia pestis complexed with coenzyme A.

PDB DOI: https://doi.org/10.2210/pdb3L92/pdb

Classification: TRANSFERASE
Organism(s): Yersinia pestis CO92
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-01-04 Released: 2010-01-19
Deposition Author(s): Osipiuk, J., Maltseva, N., Makowska-grzyska, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.192 (Depositor), 0.189 (DCC)
R-Value Work:
0.164 (Depositor), 0.163 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

X-ray crystal structure of phosphopantetheine adenylyltransferase from Yersinia pestis.

Osipiuk, J., Maltseva, N., Makowska-grzyska, M., Kwon, K., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 18.72 kDa
Atom Count: 1,595
Modeled Residue Count: 159
Deposited Residue Count: 162
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopantetheine adenylyltransferase	A	162	Yersinia pestis CO92	Mutation(s): 0 Gene Names: coaD, kdtB, y0088, YPO0053, YP_0054 EC: 2.7.7.3
UniProt
Find proteins for Q8ZJN9 (Yersinia pestis) Explore Q8ZJN9 Go to UniProtKB: Q8ZJN9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZJN9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA 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]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.192 (Depositor), 0.189 (DCC)
R-Value Work: 0.164 (Depositor), 0.163 (DCC)
R-Value Observed: 0.165 (Depositor)

Diffraction Data:

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.82	α = 90
b = 114.82	β = 90
c = 119.074	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
MOLREP	phasing
HKL-3000	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-01-19

Deposition Author(s):

Makowska-grzyska, M.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-01-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2014-10-01
Changes: Structure summary
Version 1.3: 2017-11-01
Changes: Refinement description
Version 1.4: 2023-09-06
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.