3D53 | pdb_00003d53

2.2 A crystal structure of inorganic pyrophosphatase from Rickettsia prowazekii

PDB DOI: https://doi.org/10.2210/pdb3D53/pdb

Classification: HYDROLASE
Organism(s): Rickettsia prowazekii str. Madrid E
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-05-15 Released: 2008-05-27
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.280 (Depositor), 0.280 (DCC)
R-Value Work:
0.217 (Depositor), 0.220 (DCC)
R-Value Observed:
0.220 (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

2.2 A crystal structure of inorganic pyrophosphatase from Rickettsia prowazekii.

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 118.76 kDa
Atom Count: 8,716
Modeled Residue Count: 1,016
Deposited Residue Count: 1,038
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inorganic pyrophosphatase	A, B, C, D, E A, B, C, D, E, F	173	Rickettsia prowazekii str. Madrid E	Mutation(s): 0 Gene Names: ppa, RP589 EC: 3.6.1.1
UniProt
Find proteins for Q9ZCW5 (Rickettsia prowazekii (strain Madrid E)) Explore Q9ZCW5 Go to UniProtKB: Q9ZCW5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9ZCW5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain S [auth C] SDF format, chain O [auth B] MOL2 format, chain Z [auth E] MOL2 format, chain S [auth C] MOL2 format, chain O [auth B] mmCIF format, chain Z [auth E] mmCIF format, chain S [auth C] mmCIF format, chain O [auth B]	O [auth B], S [auth C], Z [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain S [auth C] Focus chain Z [auth E] Interactions & Density Focus chain O [auth B] Focus chain S [auth C] Focus chain Z [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain X [auth E] SDF format, chain W [auth E] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain CA [auth F] SDF format, chain BA [auth F] SDF format, chain AA [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth E] MOL2 format, chain W [auth E] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain CA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain AA [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth E] mmCIF format, chain W [auth E] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain CA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth F] CA [auth F] G [auth A] H [auth A] AA [auth F], BA [auth F], CA [auth F], G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth B], P [auth C], Q [auth C], R [auth C], T [auth D], U [auth D], V [auth D], W [auth E], X [auth E], Y [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.280 (Depositor), 0.280 (DCC)
R-Value Work: 0.217 (Depositor), 0.220 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.97	α = 90
b = 115.23	β = 90
c = 139.73	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-05-27

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2008-05-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description