6KKW | pdb_00006kkw

Crystal structure of the complex of phosphopantetheine adenylyl transferase from Acinetobacter baumannii with Dephospho Coenzyme at 3.2 A resolution.

PDB DOI: https://doi.org/10.2210/pdb6KKW/pdb

Classification: TRANSFERASE
Organism(s): Acinetobacter baumannii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-07-27 Released: 2019-08-21
Deposition Author(s): Viswanathan, V., Gupta, A., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.233 (Depositor), 0.220 (DCC)
R-Value Work:
0.175 (Depositor), 0.178 (DCC)

Starting Model: experimental
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Literature

Crystal structure of the complex of phosphopantetheine adenylyl transferase from Acinetobacter baumannii with Dephospho Coenzyme at 3.2 A resolution.

Viswanathan, V., Gupta, A., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 19.2 kDa
Atom Count: 1,372
Modeled Residue Count: 163
Deposited Residue Count: 163
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopantetheine adenylyltransferase	A	163	Acinetobacter baumannii	Mutation(s): 0 Gene Names: coaD EC: 2.7.7.3
UniProt
Find proteins for B0V8I3 (Acinetobacter baumannii (strain AYE)) Explore B0V8I3 Go to UniProtKB: B0V8I3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B0V8I3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COD (Subject of Investigation/LOI) Query on COD 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]	DEPHOSPHO COENZYME A C₂₁ H₃₅ N₇ O₁₃ P₂ S KDTSHFARGAKYJN-IBOSZNHHSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL (Subject of Investigation/LOI) 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.233 (Depositor), 0.220 (DCC)
R-Value Work: 0.175 (Depositor), 0.178 (DCC)

Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 215.539	α = 90
b = 215.539	β = 90
c = 215.539	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-08-21

Deposition Author(s):

Viswanathan, V.

Revision History (Full details and data files)

Version 1.0: 2019-08-21
Type: Initial release
Version 1.1: 2023-11-22
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.