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- PDB-8ji1: Crystal structure of Ham1 from Plasmodium falciparum -

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Basic information

Entry
Database: PDB / ID: 8ji1
TitleCrystal structure of Ham1 from Plasmodium falciparum
ComponentsInosine triphosphate pyrophosphatase
KeywordsHYDROLASE / Pyrophosphohydrolase
Function / homology
Function and homology information


Purine catabolism / Ribavirin ADME / deoxyribonucleoside triphosphate catabolic process / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleotide diphosphatase / nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / nucleotide metabolic process ...Purine catabolism / Ribavirin ADME / deoxyribonucleoside triphosphate catabolic process / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleotide diphosphatase / nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / nucleotide metabolic process / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Inosine triphosphate pyrophosphatase / Ham1-like protein / Ham1 family / Inosine triphosphate pyrophosphatase-like
Similarity search - Domain/homology
Inosine triphosphate pyrophosphatase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPramanik, A. / Datta, S.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR) India
CitationJournal: To Be Published
Title: Crystal structure of Ham1 from Plasmodium falciparum
Authors: Pramanik, A. / Datta, S.
History
DepositionMay 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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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)46,2252
Polymers46,2252
Non-polymers00
Water3,405189
1
A: Inosine triphosphate pyrophosphatase

B: Inosine triphosphate pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)46,2252
Polymers46,2252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y+1/2,-z+3/21
Buried area2300 Å2
ΔGint-10 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.294, 73.658, 111.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Ham1


Mass: 23112.307 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: MAL7P1.110 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IBP3, nucleotide diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 16% PEG 4000, 100 mM Citrate buffer pH 5.5, 20% Isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS 3.0 MICROFOCUS / Wavelength: 1.53 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Jan 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.53 Å / Relative weight: 1
ReflectionResolution: 2.4→29.08 Å / Num. obs: 20443 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.998 / Net I/σ(I): 20.7
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 2080 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F95

4f95


Resolution: 2.4→26.17 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2565 1292 6.32 %
Rwork0.1946 --
obs0.1986 20443 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→26.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3173 0 0 189 3362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073247
X-RAY DIFFRACTIONf_angle_d0.8964361
X-RAY DIFFRACTIONf_dihedral_angle_d4.6982384
X-RAY DIFFRACTIONf_chiral_restr0.051462
X-RAY DIFFRACTIONf_plane_restr0.005567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.49610.2951340.23632000X-RAY DIFFRACTION93
2.4961-2.60960.25261320.23182018X-RAY DIFFRACTION93
2.6096-2.7470.31181420.23222065X-RAY DIFFRACTION95
2.747-2.91890.29481420.21422092X-RAY DIFFRACTION97
2.9189-3.1440.28861440.21022125X-RAY DIFFRACTION98
3.144-3.45970.25081440.19042148X-RAY DIFFRACTION98
3.4597-3.95890.22551460.18012159X-RAY DIFFRACTION98
3.9589-4.98210.2541500.16062219X-RAY DIFFRACTION100
4.9821-26.170.23341580.19482325X-RAY DIFFRACTION100

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