5EQT

crystal structure of the ATPase domain of PAN from Pyrococcus horikoshii

PDB DOI: https://doi.org/10.2210/pdb5EQT/pdb

Classification: HYDROLASE
Organism(s): Pyrococcus horikoshii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-11-13 Released: 2016-11-23
Deposition Author(s): Colombo, M.
Funding Organization(s): Centre Nationale de la Recherche Scientifique

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.239
R-Value Work: 0.223
R-Value Observed: 0.224

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

crystal structure of the ATPase domain of PAN from Pyrococcus horikoshii

Colombo, M., Ibrahim, Z., Flament, D., Hartlein, M., Teixeira, S., Girard, E., Gabel, F., Franzetti, B.

To be published.

Macromolecule Content

Total Structure Weight: 29.24 kDa
Atom Count: 2,006
Modelled Residue Count: 249
Deposited Residue Count: 257
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome-activating nucleotidase	A	257	Pyrococcus horikoshii	Mutation(s): 0 Gene Names: pan, PH0201
UniProt
Find proteins for O57940 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57940 Go to UniProtKB: O57940
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O57940
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.239
R-Value Work: 0.223
R-Value Observed: 0.224
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.344	α = 90
b = 46.488	β = 115.18
c = 56.428	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-11-23

Deposition Author(s):

Colombo, M.

Funding Organization	Location	Grant Number
Centre Nationale de la Recherche Scientifique	France	ANR-12-BSV8-0019-0

Revision History (Full details and data files)

Version 1.0: 2016-11-23
Type: Initial release
Version 1.1: 2019-02-20
Changes: Advisory, Data collection, Derived calculations
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description

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5EQT

crystal structure of the ATPase domain of PAN from Pyrococcus horikoshii

crystal structure of the ATPase domain of PAN from Pyrococcus horikoshii

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)