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- PDB-1ude: Crystal structure of the Inorganic pyrophosphatase from the hyper... -

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Basic information

Entry
Database: PDB / ID: 1ude
TitleCrystal structure of the Inorganic pyrophosphatase from the hyperthermophilic archaeon Pyrococcus horikoshii OT3
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / inorganic pyrophosphatase X-ray crystallographic analysis
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
Inorganic pyrophosphatase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsLiu, B. / Gao, R. / Zhou, W. / Bartlam, M. / Rao, Z.
CitationJournal: Biophys.J. / Year: 2004
Title: Crystal structure of the hyperthermophilic inorganic pyrophosphatase from the archaeon Pyrococcus horikoshii.
Authors: Liu, B. / Bartlam, M. / Gao, R. / Zhou, W. / Pang, H. / Liu, Y. / Feng, Y. / Rao, Z.
History
DepositionApr 29, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation / struct_ref_seq_dif
Item: _citation.pdbx_database_id_DOI / _citation.title / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
C: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)68,4103
Polymers68,4103
Non-polymers00
Water1,67593
1
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
C: Inorganic pyrophosphatase

A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
C: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)136,8196
Polymers136,8196
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area15360 Å2
ΔGint-70 kcal/mol
Surface area37250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.827, 86.687, 92.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a hexamer generated from the trimer in the asymmetric unit by crystallographic quadratic operations

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Components

#1: Protein Inorganic pyrophosphatase


Mass: 22803.168 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PPA / Plasmid: PET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BE21 / References: UniProt: O59570, inorganic diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 4000, Na Acetete, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 5.2 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
23.8 %PEG40001reservoir
30.1 Msodium acetate1reservoirpH5.0-5.2
40.02 M1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.66→50 Å / Num. obs: 17030 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.93 % / Rmerge(I) obs: 0.075
Reflection shellResolution: 2.66→2.9 Å / % possible all: 98
Reflection
*PLUS
Num. measured all: 118041
Reflection shell
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 4.3

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→50 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: inorganic pyrophosphatase Sulfolobus acidocaldarius (S-PPase)
RfactorNum. reflection% reflectionSelection details
Rfree0.2765 1687 10 %RANDOM
Rwork0.2324 ---
all0.24 16857 --
obs0.24 16857 98.5 %-
Refinement stepCycle: LAST / Resolution: 2.66→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4145 0 0 93 4238
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01282
X-RAY DIFFRACTIONc_angle_deg1.94722
LS refinement shellResolution: 2.66→2.83 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 268 10.6 %
Rwork0.322 2268 -
obs--90.7 %
Refinement
*PLUS
Num. reflection obs: 117986
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6

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