8XSC | pdb_00008xsc

PPAT in complex with Ppant

PDB DOI: https://doi.org/10.2210/pdb8XSC/pdb

Classification: TRANSFERASE
Organism(s): Helicobacter pylori 26695
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-01-09 Released: 2024-10-30
Deposition Author(s): Yin, H.S.
Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.219 (Depositor), 0.219 (DCC)
R-Value Work:
0.160 (Depositor), 0.164 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

PPAT in complex with Ppant

Yin, H.S.

To be published.

Macromolecule Content

Total Structure Weight: 35.74 kDa
Atom Count: 2,602
Modeled Residue Count: 314
Deposited Residue Count: 314
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopantetheine adenylyltransferase	A, B	157	Helicobacter pylori 26695	Mutation(s): 0 Gene Names: coaD, kdtB, HP_1475 EC: 2.7.7.3
UniProt
Find proteins for O26010 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O26010 Go to UniProtKB: O26010
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O26010
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PNS (Subject of Investigation/LOI) Query on PNS 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]	4'-PHOSPHOPANTETHEINE C₁₁ H₂₃ N₂ O₇ P S JDMUPRLRUUMCTL-VIFPVBQESA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.219 (Depositor), 0.219 (DCC)
R-Value Work: 0.160 (Depositor), 0.164 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.072	α = 90
b = 79.072	β = 90
c = 147.274	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	--

Revision History (Full details and data files)

Version 1.0: 2024-10-30
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.