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- PDB-4dk4: Crystal Structure of Trypanosoma brucei dUTPase with dUpNp, Ca2+ ... -

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Basic information

Entry
Database: PDB / ID: 4dk4
TitleCrystal Structure of Trypanosoma brucei dUTPase with dUpNp, Ca2+ and Na+
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: 1.9 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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

Downloads & links

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Assembly

Deposited unit
A: Deoxyuridine triphosphatase
B: Deoxyuridine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,38910
Polymers64,4092
Non-polymers9818
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-110 kcal/mol
Surface area17820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.840, 83.190, 91.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Deoxyuridine triphosphatase / deoxyuridine triphosphate nucleotidohydrolase


Mass: 32204.271 Da / Num. of mol.: 2
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-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.: 2 / Source method: obtained synthetically / Formula: C9H15N3O10P2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 1.73 Å3/Da / Density % sol: 29 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% w/v PEG1500, 0.1 M PCB buffer, 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: 1.9→61.455 Å / Num. all: 36008 / Num. obs: 36008 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.3 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-27.30.5441.43742051500.544100
2-2.127.20.3332.33565049180.333100
2.12-2.277.20.2173.53341246110.217100
2.27-2.457.20.1594.83123843230.159100
2.45-2.697.20.1156.42870139890.115100
2.69-37.20.0858.52579536060.085100
3-3.477.10.0778.42273532230.077100
3.47-4.2513.60.0966.63734027510.096100
4.25-6.0113.40.0946.42911821650.094100
6.01-58.8412.50.053111592312720.05399.9

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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
APEXdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OGK

1ogk


Resolution: 1.9→61.455 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.183 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 1793 5 %RANDOM
Rwork0.1774 ---
all0.1801 36008 --
obs0.1801 35890 99.82 %-
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: 22.5685 Å2 / Biso min: 3.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20 Å2
2--0.66 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→61.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3364 0 54 144 3562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223493
X-RAY DIFFRACTIONr_bond_other_d0.0010.022219
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9534769
X-RAY DIFFRACTIONr_angle_other_deg0.98235421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.285431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59724.74154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80615534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0521513
X-RAY DIFFRACTIONr_chiral_restr0.0910.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023889
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02704
X-RAY DIFFRACTIONr_mcbond_it12.6621.52161
X-RAY DIFFRACTIONr_mcbond_other0.4131.5878
X-RAY DIFFRACTIONr_mcangle_it15.02823437
X-RAY DIFFRACTIONr_scbond_it31.33431332
X-RAY DIFFRACTIONr_scangle_it17.9954.51332
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 133 -
Rwork0.236 2450 -
all-2583 -
obs--99.85 %

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