5UCQ | pdb_00005ucq

The structure of archaeal Inorganic Pyrophosphatase in complex with pyrophosphate

PDB DOI: https://doi.org/10.2210/pdb5UCQ/pdb
Entry: 5UCQ supersedes: 3Q9M

Classification: HYDROLASE
Organism(s): Thermococcus thioreducens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-12-22 Released: 2017-02-08
Deposition Author(s): Inoguchi, N., Hughes, R.C., Meehan, E.J., Ng, J.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.140 (Depositor), 0.141 (DCC)
R-Value Work:
0.109 (Depositor), 0.112 (DCC)
R-Value Observed:
0.110 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The structure of archaeal Inorganic Pyrophosphatase in complex with pyrophosphate

Inoguchi, N., Hughes, R.C., Meehan, E.J., Ng, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 64.23 kDa
Atom Count: 5,599
Modeled Residue Count: 526
Deposited Residue Count: 534
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inorganic pyrophosphatase	A, B, C	178	Thermococcus thioreducens	Mutation(s): 0 Gene Names: ppa EC: 3.6.1.1
UniProt
Find proteins for H0USY5 (Thermococcus thioreducens) Explore H0USY5 Go to UniProtKB: H0USY5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H0USY5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POP Query on POP Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain S [auth B] SDF format, chain Z [auth C] MOL2 format, chain K [auth A] MOL2 format, chain S [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain K [auth A] mmCIF format, chain S [auth B] mmCIF format, chain Z [auth C]	K [auth A], S [auth B], Z [auth C]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Interactions Focus chain K [auth A] Focus chain S [auth B] Focus chain Z [auth C] Interactions & Density Focus chain K [auth A] Focus chain S [auth B] Focus chain Z [auth C]
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	G [auth A] H [auth A] I [auth A] O [auth B] P [auth B] G [auth A], H [auth A], I [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], X [auth C], Y [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain X [auth C] Focus chain Y [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C]	D [auth A] E [auth A] F [auth A] L [auth B] M [auth B] D [auth A], E [auth A], F [auth A], L [auth B], M [auth B], N [auth B], U [auth C], V [auth C], W [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B] mmCIF format, chain T [auth B]	T [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.140 (Depositor), 0.141 (DCC)
R-Value Work: 0.109 (Depositor), 0.112 (DCC)
R-Value Observed: 0.110 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.161	α = 90
b = 100.161	β = 90
c = 97.801	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHENIX	phasing
HKL-2000	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-02-08

Deposition Author(s):

This entry supersedes: 3Q9M

Revision History (Full details and data files)

Version 1.0: 2017-02-08
Type: Initial release
Version 1.1: 2017-05-03
Changes: Advisory
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description