9IYG | pdb_00009iyg

Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the 17-mer expression tag bound in the substrate binding site of a neighbouring molecule at 2.60 A resolution.

PDB DOI: https://doi.org/10.2210/pdb9IYG/pdb

Classification: TRANSFERASE
Organism(s): Enterobacter sp. 638
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-07-30 Released: 2024-08-21
Deposition Author(s): Ahmad, N., Sharma, P., Sharma, S., Singh, T.P.
Funding Organization(s): Indian Council of Medical Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.270 (Depositor), 0.270 (DCC)
R-Value Work:
0.227 (Depositor), 0.234 (DCC)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the 17-mer expression tag bound in the substrate binding site of a neighbouring molecule at 2.60 A resolution.

Ahmad, N., Sharma, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 118.03 kDa
Atom Count: 8,271
Modeled Residue Count: 988
Deposited Residue Count: 1,056
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopantetheine adenylyltransferase	A, B, C, D, E A, B, C, D, E, F	176	Enterobacter sp. 638	Mutation(s): 0 Gene Names: coaD, Ent638_0105 EC: 2.7.7.3
UniProt
Find proteins for A4W515 (Enterobacter sp. (strain 638)) Explore A4W515 Go to UniProtKB: A4W515
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4W515
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain M [auth F] SDF format, chain L [auth E] SDF format, chain J [auth D] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain M [auth F] MOL2 format, chain L [auth E] MOL2 format, chain J [auth D] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain M [auth F] mmCIF format, chain L [auth E] mmCIF format, chain J [auth D] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A] H [auth B] I [auth C] J [auth D] L [auth E] G [auth A], H [auth B], I [auth C], J [auth D], L [auth E], M [auth F]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain L [auth E] Focus chain M [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain L [auth E] Focus chain M [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.270 (Depositor), 0.270 (DCC)
R-Value Work: 0.227 (Depositor), 0.234 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.271	α = 90
b = 79.846	β = 93.354
c = 107.541	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
autoPROC	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Indian Council of Medical Research	India	I-1251

Revision History (Full details and data files)

Version 1.0: 2024-08-21
Type: Initial release

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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.