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- PDB-4dk2: Crystal Structure of Open Trypanosoma brucei dUTPase -

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Basic information

Entry
Database: PDB / ID: 4dk2
TitleCrystal Structure of Open Trypanosoma brucei dUTPase
ComponentsDeoxyuridine triphosphataseDUTP diphosphatase
KeywordsHYDROLASE / all alpha NTP pyrophosphohydrolase / all alpha NTP pyrophosphatase / dUTP and Mg2+ binding
Function / homology
Function and homology information


dUTP diphosphatase / dUTP diphosphatase activity / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
all-alpha NTP pyrophosphatase / Type II deoxyuridine triphosphatase / all-alpha NTP pyrophosphatases / Type II deoxyuridine triphosphatase / dUTPase/dCTP pyrophosphatase / dUTPase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Deoxyuridine triphosphatase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsHemsworth, G.R. / Gonzalez-Pacanowska, D. / Wilson, K.S.
CitationJournal: Biochem.J. / Year: 2013
Title: On the catalytic mechanism of dimeric dUTPases.
Authors: Hemsworth, G.R. / Gonzalez-Pacanowska, D. / Wilson, K.S.
History
DepositionFeb 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Nov 6, 2013Group: Database references
Revision 1.3Sep 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: Deoxyuridine triphosphatase


Theoretical massNumber of molelcules
Total (without water)33,1701
Polymers33,1701
Non-polymers00
Water3,171176
1
A: Deoxyuridine triphosphatase

A: Deoxyuridine triphosphatase


Theoretical massNumber of molelcules
Total (without water)66,3412
Polymers66,3412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3960 Å2
ΔGint-21 kcal/mol
Surface area23940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.010, 47.020, 63.460
Angle α, β, γ (deg.)90.00, 89.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-380-

HOH

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Components

#1: Protein Deoxyuridine triphosphatase / DUTP diphosphatase / deoxyuridine triphosphate nucleotidohydrolase


Mass: 33170.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: 427 / Gene: Tb927.7.5160 / Plasmid: pET-YSBLLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q57ZH3, dUTP diphosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.11 Å3/Da / Density % sol: 41.82 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 25% PEG1500, 0.1 M MMT buffer, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2011
RadiationMonochromator: ACCEL fixed exit double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.47→42.05 Å / Num. all: 47254 / Num. obs: 47254 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 8.3
Reflection shellResolution: 1.47→1.55 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6789 / Rsym value: 0.493 / % possible all: 98.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OGL

1ogl


Resolution: 1.47→42.05 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.221 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.065 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21068 2368 5 %RANDOM
Rwork0.17774 ---
obs0.17933 44812 99.33 %-
all-47254 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.009 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å2-0.26 Å2
2--1.05 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.47→42.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 0 176 2184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222058
X-RAY DIFFRACTIONr_bond_other_d0.0010.021336
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9392806
X-RAY DIFFRACTIONr_angle_other_deg0.95133253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.095258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06424.23992
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64215314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6611510
X-RAY DIFFRACTIONr_chiral_restr0.0930.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212321
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02425
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it61.4941.51294
X-RAY DIFFRACTIONr_mcbond_other10.2721.5523
X-RAY DIFFRACTIONr_mcangle_it48.88422061
X-RAY DIFFRACTIONr_scbond_it65.7483764
X-RAY DIFFRACTIONr_scangle_it37.0154.5745
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.47→1.506 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 157 -
Rwork0.298 3226 -
obs--97.18 %

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