5TY5 | pdb_00005ty5

Neutron structure from microgravity-grown crystals of Inorganic Pyrophosphatase from Thermococcus theoreducens

PDB DOI: https://doi.org/10.2210/pdb5TY5/pdb

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

Deposited: 2016-11-18 Released: 2017-11-22
Deposition Author(s): Inoguchi, N., Coates, L., Morris, M.L., Singhal, A., Monaco, D.A., Garcia-Ruiz, J.M., Pusey, M.L., Ng, J.D.
Funding Organization(s): Center for the Advancement of Science in Space (CASIS)

Experimental Data Snapshot

Method: NEUTRON DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.252 (Depositor)
R-Value Work:
0.239 (Depositor)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Structure-function analysis of the neutron crystallographic structure of inorganic pyrophosphatase determined from microgravity-grown crystals

Inoguchi, N., Coates, L., Meilleur, F., Morris, M.L., Singhal, A., Barcena, J., Garcia-Ruiz, J.M., Pusey, M.L., Ng, J.D.

(2017) Acta Crystallogr A 73: 132-132

DOI: https://doi.org/10.1107/S0108767317098695

Macromolecule Content

Total Structure Weight: 125.29 kDa
Atom Count: 9,025
Modeled Residue Count: 1,044
Deposited Residue Count: 1,068
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	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

Experimental Data & Validation

Experimental Data

Method: NEUTRON DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.252 (Depositor)
R-Value Work: 0.239 (Depositor)
R-Value Observed: 0.239 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.93	α = 90
b = 95.03	β = 98.13
c = 113.5	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-11-22

Deposition Author(s):

Garcia-Ruiz, J.M.

Funding Organization	Location	Grant Number
Center for the Advancement of Science in Space (CASIS)	United States	GA-2013-100

Revision History (Full details and data files)

Version 1.0: 2017-11-22
Type: Initial release
Version 1.1: 2019-01-09
Changes: Data collection, Database references, Experimental preparation
Version 1.2: 2023-10-04
Changes: Data collection, Database references, 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.