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- PDB-4dl8: Crystal structure of Trypanosoma brucei dUTPase with dUMP, planar... -

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Basic information

Entry
Database: PDB / ID: 4dl8
TitleCrystal structure of Trypanosoma brucei dUTPase with dUMP, planar [AlF3-OPO3] transition state analogue, Mg2+, and Na+
ComponentsDeoxyuridine triphosphataseDUTP diphosphatase
KeywordsHYDROLASE / all alpha NTP pyrophosphohydrolase / all alpha NTP pyrophosphatase
Function / homology
Function and homology information


dUTP diphosphatase / dUTP diphosphatase activity / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
all-alpha NTP pyrophosphatase fold / Type II deoxyuridine triphosphatase / dUTPase/dCTP pyrophosphatase / dUTPase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ALUMINUM FLUORIDE / PHOSPHATE ION / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Deoxyuridine triphosphatase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / REFINED 4DKB / Resolution: 1.698 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 6, 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 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxyuridine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7637
Polymers32,2041
Non-polymers5596
Water2,990166
1
A: Deoxyuridine triphosphatase
hetero molecules

A: Deoxyuridine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,52614
Polymers64,4092
Non-polymers1,11712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area5830 Å2
ΔGint-106 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.590, 68.590, 123.759
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 32204.271 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

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Non-polymers , 6 types, 172 molecules

#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium sulfate, 0.1 M Bis-Tris propane, pH 6.5, 20% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 28, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.698→28.203 Å / Num. all: 33398 / Num. obs: 33398 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 15.7 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 23.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.698-1.7915.70.9230.87417947100.92398.4
1.79-1.9150.5861.36810045350.586100
1.9-2.03160.3612.16873242870.361100
2.03-2.1916.70.213.76672040010.21100
2.19-2.416.30.145.46037736970.14100
2.4-2.6815.20.0957.85117233630.095100
2.68-3.115.70.06211.44702629880.062100
3.1-3.816.20.04215.34165725670.042100
3.8-5.3714.40.03218.82933320400.03299.9
5.37-29.77315.10.0315.61830212100.0399.4

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
REFMAC5.5.0109phasing
RefinementMethod to determine structure: REFINED 4DKB
Starting model: PDB ENTRY 4DKB

4dkb


Resolution: 1.698→28.2 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1759 / WRfactor Rwork: 0.1545 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8909 / SU B: 1.681 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0828 / SU Rfree: 0.0837 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 1661 5 %RANDOM
Rwork0.1667 ---
all0.1681 33398 --
obs0.1681 33293 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 424.2 Å2 / Biso mean: 25.9297 Å2 / Biso min: 8.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2--0.5 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.698→28.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 32 166 1962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0271836
X-RAY DIFFRACTIONr_bond_other_d0.0010.021184
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9922493
X-RAY DIFFRACTIONr_angle_other_deg0.94432893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1065222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52724.88184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82515297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.339158
X-RAY DIFFRACTIONr_chiral_restr0.0910.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022022
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02360
X-RAY DIFFRACTIONr_mcbond_it20.911.51114
X-RAY DIFFRACTIONr_mcbond_other0.6061.5452
X-RAY DIFFRACTIONr_mcangle_it18.15521785
X-RAY DIFFRACTIONr_scbond_it21.2863722
X-RAY DIFFRACTIONr_scangle_it17.6054.5708
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 121 -
Rwork0.263 2237 -
all-2358 -
obs--97.44 %

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