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- PDB-4dkb: Crystal Structure of Trypanosoma brucei dUTPase with dUpNp and Ca2+ -

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Basic information

Entry
Database: PDB / ID: 4dkb
TitleCrystal Structure of Trypanosoma brucei dUTPase with dUpNp and Ca2+
ComponentsDeoxyuridine triphosphatase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / all alpha NTP pyrophosphohydrolase / all alpha NTP pyrophosphatase / HYDROLASE-HYDROLASE INHIBITOR complex
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
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-DIPHOSPHATE / Deoxyuridine triphosphatase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.831 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 ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / 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: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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)32,6724
Polymers32,2041
Non-polymers4673
Water2,432135
1
A: Deoxyuridine triphosphatase
hetero molecules

A: Deoxyuridine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3438
Polymers64,4092
Non-polymers9356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area4650 Å2
ΔGint-83 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.470, 68.470, 123.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Deoxyuridine triphosphatase / 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-YSBLLIC3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q57ZH3, dUTP diphosphatase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-DUN / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-DIPHOSPHATE / 2,4(1H,3H)-PYRIMIDINEDIONE / 1-[2-DEOXY-5-O-[HYDROXY(PHOSPHONOAMINO)PHOSPHINYL]-BETA-D-ERYTHRO-PENTOFURANOSYL]-


Mass: 387.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N3O10P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% w/v PEG3350, 0.2 M ammonium citrate tribasic, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2010
RadiationMonochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.831→48.416 Å / Num. all: 26775 / Num. obs: 26775 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.7 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 18.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.831-1.9313.10.5841.35015038240.584100
1.93-2.0514.20.37225154536230.372100
2.05-2.1914.20.2243.34867634250.224100
2.19-2.3614.10.1554.84517731940.155100
2.36-2.5914.10.1225.94154329490.122100
2.59-2.913.90.08783746926890.087100
2.9-3.3413.80.0699.23307323990.069100
3.34-4.0913.30.0777.72739120540.077100
4.09-5.7912.50.1015.62037916340.101100
5.79-48.41612.40.03814.5122439840.03899.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DK4

4dk4


Resolution: 1.831→48.416 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.031 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1978 1331 5 %RANDOM
Rwork0.1688 ---
all0.1702 26675 --
obs0.1702 26675 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 200 Å2 / Biso mean: 21.4041 Å2 / Biso min: 5.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.831→48.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 26 135 1922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221826
X-RAY DIFFRACTIONr_bond_other_d0.0010.021178
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9542489
X-RAY DIFFRACTIONr_angle_other_deg0.9532876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9185221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89924.88486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11115293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.979158
X-RAY DIFFRACTIONr_chiral_restr0.0930.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022022
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
X-RAY DIFFRACTIONr_mcbond_it11.511.51108
X-RAY DIFFRACTIONr_mcbond_other0.5751.5450
X-RAY DIFFRACTIONr_mcangle_it12.52421776
X-RAY DIFFRACTIONr_scbond_it28.3363718
X-RAY DIFFRACTIONr_scangle_it24.3934.5713
LS refinement shellResolution: 1.831→1.879 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 85 -
Rwork0.276 1844 -
all-1929 -
obs-1844 99.84 %

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