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- PDB-4f95: Crystal structure of human inosine triphosphate pyrophosphatase P... -

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Basic information

Entry
Database: PDB / ID: 4f95
TitleCrystal structure of human inosine triphosphate pyrophosphatase P32T variant
ComponentsInosine triphosphate pyrophosphatase
KeywordsHYDROLASE
Function / homology
Function and homology information


ITP catabolic process / deoxyribonucleoside triphosphate catabolic process / XTP/dITP diphosphatase / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / Ribavirin ADME / Purine catabolism ...ITP catabolic process / deoxyribonucleoside triphosphate catabolic process / XTP/dITP diphosphatase / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / Ribavirin ADME / Purine catabolism / chromosome organization / nucleotide binding / intracellular membrane-bounded organelle / nucleoplasm / metal ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Inosine triphosphate pyrophosphatase / Ham1-like protein / Ham1 family / Maf protein - #10 / Inosine triphosphate pyrophosphatase-like / Maf protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Inosine triphosphate pyrophosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsSimone, P.D. / Pavlov, Y.I. / Borgstahl, G.E.O.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: The human ITPA polymorphic variant P32T is destabilized by the unpacking of the hydrophobic core.
Authors: Simone, P.D. / Struble, L.R. / Kellezi, A. / Brown, C.A. / Grabow, C.E. / Khutsishvili, I. / Marky, L.A. / Pavlov, Y.I. / Borgstahl, G.E.
History
DepositionMay 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inosine triphosphate pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)21,7551
Polymers21,7551
Non-polymers00
Water1,22568
1
A: Inosine triphosphate pyrophosphatase

A: Inosine triphosphate pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)43,5102
Polymers43,5102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2210 Å2
ΔGint-17 kcal/mol
Surface area17850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.020, 104.420, 50.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-233-

HOH

21A-259-

HOH

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Components

#1: Protein Inosine triphosphate pyrophosphatase / ITPase / Inosine triphosphatase / Non-canonical purine NTP pyrophosphatase / Non-standard purine ...ITPase / Inosine triphosphatase / Non-canonical purine NTP pyrophosphatase / Non-standard purine NTP pyrophosphatase / Nucleoside-triphosphate diphosphatase / Nucleoside-triphosphate pyrophosphatase / NTPase / Putative oncogene protein hlc14-06-p


Mass: 21754.893 Da / Num. of mol.: 1 / Mutation: P32T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C20orf37, ITPA, ITPA (P32T MUTANT), My049, OK/SW-cl.9 / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2(DE3)
References: UniProt: Q9BY32, nucleoside-triphosphate diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 1.87 Å3/Da / Density % sol: 34.38 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6.667
Details: 24.4% PEG 3350, 0.1 M BIS-TRIS, 10 MM BETA-MERCAPTOETHANOL, pH 6.667, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 29, 2010
RadiationMonochromator: OSMIC VARIMAX CONFOCAL MAX-FLUX OPTIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.07→29.74 Å / Num. all: 10531 / Num. obs: 10531 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.66 % / Biso Wilson estimate: 44.886 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.9
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 3.71 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(PHENIX.REFINE: 1.7.3_928)refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I5D

2i5d


Resolution: 2.07→29.736 Å / SU ML: 0.37 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 32.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3079 501 4.77 %Random
Rwork0.2341 ---
all0.2373 10495 --
obs0.2373 10495 99.73 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.9 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 49 Å2
Baniso -1Baniso -2Baniso -3
1-2.1161 Å2-0 Å2-0 Å2
2---4.5889 Å20 Å2
3---2.4728 Å2
Refinement stepCycle: LAST / Resolution: 2.07→29.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1477 0 0 68 1545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091547
X-RAY DIFFRACTIONf_angle_d1.2522100
X-RAY DIFFRACTIONf_dihedral_angle_d17.112582
X-RAY DIFFRACTIONf_chiral_restr0.079225
X-RAY DIFFRACTIONf_plane_restr0.005280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0701-2.27830.40341270.36322417X-RAY DIFFRACTION100
2.2783-2.60780.4071210.28622460X-RAY DIFFRACTION100
2.6078-3.28490.36281290.2452486X-RAY DIFFRACTION100
3.2849-29.73870.25511240.20592631X-RAY DIFFRACTION100

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