3OTW

Structural and Functional Studies of Helicobacter pylori Wild-Type and Mutated Proteins Phosphopantetheine adenylyltransferase

PDB DOI: https://doi.org/10.2210/pdb3OTW/pdb

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

Deposited: 2010-09-14 Released: 2011-09-14
Deposition Author(s): Yin, H.S., Cheng, C.S., Chen, C.G., Luo, Y.C., Chen, W.T., Cheng, S.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.222
R-Value Work: 0.186
R-Value Observed: 0.188

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural and Functional Studies of Helicobacter pylori Wild-Type and Mutated Proteins Phosphopantetheine adenylyltransferase

Yin, H.S., Cheng, C.S., Chen, C.G., Luo, Y.C., Chen, W.T., Cheng, S.Y.

To be published.

Macromolecule Content

Total Structure Weight: 116.4 kDa
Atom Count: 8,355
Modelled Residue Count: 937
Deposited Residue Count: 978
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopantetheine adenylyltransferase	A, B, C, D, E A, B, C, D, E, F	163	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O26010
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain R [auth E] SDF format, chain K [auth B] SDF format, chain S [auth F] MOL2 format, chain H [auth A] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain R [auth E] MOL2 format, chain K [auth B] MOL2 format, chain S [auth F] mmCIF format, chain H [auth A] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain R [auth E] mmCIF format, chain K [auth B] mmCIF format, chain S [auth F]	H [auth A] K [auth B] M [auth C] O [auth D] R [auth E] H [auth A], K [auth B], M [auth C], O [auth D], R [auth E], S [auth F]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain R [auth E] Focus chain S [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain R [auth E] Focus chain S [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain Q [auth E] SDF format, chain L [auth C] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain L [auth C] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth E] mmCIF format, chain L [auth C]	G [auth A] I [auth B] J [auth B] L [auth C] N [auth D] G [auth A], I [auth B], J [auth B], L [auth C], N [auth D], P [auth E], Q [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth E] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.222
R-Value Work: 0.186
R-Value Observed: 0.188
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.419	α = 90
b = 119.846	β = 90
c = 124.573	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-09-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-09-14
Type: Initial release
Version 1.1: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description