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- PDB-2car: Crystal Structure Of Human Inosine Triphosphatase -

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Basic information

Entry
Database: PDB / ID: 2car
TitleCrystal Structure Of Human Inosine Triphosphatase
ComponentsINOSINE TRIPHOSPHATE PYROPHOSPHATASE
KeywordsHYDROLASE / INOSINE TRIPHOSPHATE PYROPHOSPHOHYDROLASE / INOSINE TRIPHOSPHATASE DEFICIENCY / ITP / IMP / DISEASE MUTATION / NUCLEOTIDE METABOLISM
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 / cytoplasm / cytosol
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsStenmark, P. / Kursula, P. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. ...Stenmark, P. / Kursula, P. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Hogbom, M. / Holmberg Schiavone, L. / Kotenyova, T. / Nilsson-Ehle, P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Schuler, H. / Sundstrom, M. / Thorsell, A.G. / van den Berg, S. / Weigelt, J. / Nordlund, P.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal Structure of Human Inosine Triphosphatase. Substrate Binding and Implication of the Inosine Triphosphatase Deficiency Mutation P32T.
Authors: Stenmark, P. / Kursula, P. / Flodin, S. / Graslund, S. / Landry, R. / Nordlund, P. / Schuler, H.
History
DepositionDec 22, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INOSINE TRIPHOSPHATE PYROPHOSPHATASE
B: INOSINE TRIPHOSPHATE PYROPHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)43,2262
Polymers43,2262
Non-polymers00
Water11,674648
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)31.230, 105.000, 50.140
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99999, -0.00266, 0.00228), (0.00266, -1, 0.00148), (0.00227, 0.00149, 1)
Vector: 78.04881, 104.64251, -0.1113)

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Components

#1: Protein INOSINE TRIPHOSPHATE PYROPHOSPHATASE / INOSINE TRIPHOSPHATASE / ITPASE / ONCOGENE PROTEIN HLC14-06-P


Mass: 21612.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A-LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9BY32, nucleoside-triphosphate diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHYDROLYZES ITP AND DITP TO THEIR RESPECTIVE MONOPHOSPHATE DERIVATIVES

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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: 1.9 Å3/Da / Density % sol: 35 %
Description: THE CRYSTAL WAS PSEUDO MEROHEDRALLY TWINNED. THE TWINNING OPERATION IS -K,-H, L. THE TWINNING FRACTION IS 0.50. THE TEST SET IS NOT RELATED TO THE WORKING SET BY THE TWIN OPERATION.
Crystal growDetails: 0.2 M POTASSIUM CHLORIDE, 27 % (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9781
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 22, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9781 Å / Relative weight: 1
ReflectionResolution: 1.09→40 Å / Num. obs: 123899 / % possible obs: 92.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.8
Reflection shellResolution: 1.09→1.2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.8 / % possible all: 86.6

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
MOLREPphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B78

1b78


Resolution: 1.09→40 Å / Num. parameters: 35184 / Num. restraintsaints: 45253 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1534 2636 2.2 %RANDOM
all0.0974 121263 --
obs0.0954 -90.7 %-
Refine analyzeNum. disordered residues: 35 / Occupancy sum hydrogen: 2881 / Occupancy sum non hydrogen: 3674.5
Refinement stepCycle: LAST / Resolution: 1.09→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3028 0 0 648 3676
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.041
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0311
X-RAY DIFFRACTIONs_zero_chiral_vol0.101
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.095
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.032
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.066
X-RAY DIFFRACTIONs_approx_iso_adps0.098

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