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- PDB-5ty5: Neutron structure from microgravity-grown crystals of Inorganic P... -

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Basic information

Entry
Database: PDB / ID: 5ty5
TitleNeutron structure from microgravity-grown crystals of Inorganic Pyrophosphatase from Thermococcus theoreducens
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / Neutron / thermophile / microgravity
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Inorganic Pyrophosphatase / Inorganic pyrophosphatase / Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DEUTERATED WATER / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesThermococcus thioreducens (archaea)
MethodNEUTRON DIFFRACTION / Resolution: 2.3 Å
AuthorsInoguchi, N. / Coates, L. / Morris, M.L. / Singhal, A. / Monaco, D.A. / Garcia-Ruiz, J.M. / Pusey, M.L. / Ng, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Center for the Advancement of Science in Space (CASIS)GA-2013-100 United States
CitationJournal: Acta Crystallogr.,Sect.A / Year: 2017
Title: Structure-function analysis of the neutron crystallographic structure of inorganic pyrophosphatase determined from microgravity-grown crystals
Authors: Inoguchi, N. / Coates, L. / Meilleur, F. / Morris, M.L. / Singhal, A. / Barcena, J. / Garcia-Ruiz, J.M. / Pusey, M.L. / Ng, J.D.
History
DepositionNov 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / citation_author / exptl_crystal_grow
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _exptl_crystal_grow.method
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
C: Inorganic pyrophosphatase
D: Inorganic pyrophosphatase
E: Inorganic pyrophosphatase
F: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)125,2856
Polymers125,2856
Non-polymers00
Water6,936385
1
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
C: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)62,6433
Polymers62,6433
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-33 kcal/mol
Surface area21300 Å2
MethodPISA
2
D: Inorganic pyrophosphatase
E: Inorganic pyrophosphatase
F: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)62,6433
Polymers62,6433
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-33 kcal/mol
Surface area21590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.930, 95.030, 113.500
Angle α, β, γ (deg.)90.00, 98.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Inorganic pyrophosphatase / / Pyrophosphate phospho-hydrolase


Mass: 20880.885 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus thioreducens (archaea) / Gene: ppa / Production host: Escherichia coli (E. coli) / References: UniProt: H0USY5, inorganic diphosphatase
#2: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 0.478 %
Crystal growTemperature: 298 K / Method: counter-diffusion / pH: 4.7
Details: sodium acetate, PEG 8000, calcium chloride, sodium chloride, pyrophosphate

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SPALLATION SOURCE / Site: ORNL Spallation Neutron Source / Beamline: MANDI / Wavelength: 2-4
DetectorType: ORNL ANGER CAMERA / Detector: AREA DETECTOR / Date: Nov 3, 2014
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
121
241
ReflectionResolution: 2.3→14.78 Å / Num. obs: 36592 / % possible obs: 74.19 % / Redundancy: 2.63 % / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.106 / Net I/σ(I): 7.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.88 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 3 / Num. unique obs: 2955 / Rpim(I) all: 0.171 / % possible all: 60.55

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
LAUENORMdata scaling
RefinementStarting model: 3I98

3i98


Resolution: 2.3→14.78 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 3.39 / Phase error: 23.46
RfactorNum. reflection% reflection
Rfree0.252 1829 5 %
Rwork0.239 --
obs0.239 36580 74.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0119055
NEUTRON DIFFRACTIONf_angle_d0.61933790
NEUTRON DIFFRACTIONf_dihedral_angle_d16.6545233
NEUTRON DIFFRACTIONf_chiral_restr0.0461239
NEUTRON DIFFRACTIONf_plane_restr0.0033179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.36210.30481140.31112157NEUTRON DIFFRACTION60
2.3621-2.43130.31941140.30522184NEUTRON DIFFRACTION61
2.4313-2.50940.31181180.29792247NEUTRON DIFFRACTION62
2.5094-2.59860.29031190.29032237NEUTRON DIFFRACTION63
2.5986-2.70210.29141240.29692363NEUTRON DIFFRACTION66
2.7021-2.82420.29031300.28682471NEUTRON DIFFRACTION68
2.8242-2.9720.31031360.27052601NEUTRON DIFFRACTION72
2.972-3.15650.24981450.26122738NEUTRON DIFFRACTION77
3.1565-3.39750.24931520.26152898NEUTRON DIFFRACTION80
3.3975-3.73440.22381650.22793133NEUTRON DIFFRACTION87
3.7344-4.26330.18421710.20223252NEUTRON DIFFRACTION90
4.2633-5.32910.24071760.20533337NEUTRON DIFFRACTION92
5.3291-14.77480.24621650.20343133NEUTRON DIFFRACTION85

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