3EMJ | pdb_00003emj

2.2 A crystal structure of inorganic pyrophosphatase from rickettsia prowazekii (p21 form)

PDB DOI: https://doi.org/10.2210/pdb3EMJ/pdb

Classification: HYDROLASE
Organism(s): Rickettsia prowazekii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-09-24 Released: 2008-10-07
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:
0.267 (Depositor), 0.251 (DCC)
R-Value Work:
0.227 (Depositor), 0.234 (DCC)
R-Value Observed:
0.229 (Depositor)

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

Literature

2.2 A crystal structure of inorganic pyrophosphatase from rickettsia prowazekii (p21 form)

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 235.95 kDa
Atom Count: 16,189
Modeled Residue Count: 1,978
Deposited Residue Count: 2,076
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inorganic pyrophosphatase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	173	Rickettsia prowazekii	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ZCW5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain N [auth L] SDF format, chain M [auth E] MOL2 format, chain N [auth L] MOL2 format, chain M [auth E] mmCIF format, chain N [auth L] mmCIF format, chain M [auth E]	M [auth E], N [auth L]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain M [auth E] Focus chain N [auth L] Interactions & Density Focus chain M [auth E] Focus chain N [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.267 (Depositor), 0.251 (DCC)
R-Value Work: 0.227 (Depositor), 0.234 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.96	α = 90
b = 107.35	β = 96.05
c = 128.42	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-10-07

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2008-10-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.