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- PDB-4dlc: Crystal Structure of Trypanosoma brucei dUTPase with dUMP, MgF3- ... -

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Basic information

Entry
Database: PDB / ID: 4dlc
TitleCrystal Structure of Trypanosoma brucei dUTPase with dUMP, MgF3- transition state analogue, and Mg2+
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
TRIFLUOROMAGNESATE / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Deoxyuridine triphosphatase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / REFINED 4DKB / Resolution: 1.759 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.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_comp_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

Downloads & links

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Assembly

Deposited unit
A: Deoxyuridine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6676
Polymers32,2041
Non-polymers4625
Water2,864159
1
A: Deoxyuridine triphosphatase
hetero molecules

A: Deoxyuridine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,33312
Polymers64,4092
Non-polymers92510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area5300 Å2
ΔGint-78 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.280, 68.280, 123.660
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 / 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
#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-MGF / TRIFLUOROMAGNESATE


Mass: 81.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F3Mg
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium/potassium tartrate, 0.1 M Bis-Tris propane, pH 8.5, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.759→48.281 Å / Num. all: 29775 / Num. obs: 29775 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.7 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.759-1.812.20.78112636021690.78199.8
1.8-1.8513.40.5871.32813620990.58799.6
1.85-1.9113.30.4791.62720120420.47999.9
1.91-1.9713.10.38522593619860.38599.8
1.97-2.03130.2972.62495419210.29799.9
2.03-2.112.40.24832334418780.24899.7
2.1-2.1812.20.1794.32207118160.17999.9
2.18-2.2713.20.1445.32312717510.14499.9
2.27-2.3713.20.1196.52216016780.11999.9
2.37-2.4913.10.1017.62116016140.101100
2.49-2.6212.80.0878.71973115390.08799.9
2.62-2.7811.50.0769.61659214400.076100
2.78-2.9713.20.0611.71836513920.0699.9
2.97-3.2113.10.05213.41691512880.052100
3.21-3.5212.70.04713.51501811860.04799.8
3.52-3.9311.60.04514.41269710940.04599.8
3.93-4.54120.04115.2116579750.04199.9
4.54-5.5612.50.03716.4104418330.03799.9
5.56-7.8711.10.0351774766740.03599.8
7.87-45.83210.80.03318.243304000.03397.6

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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: 1.759→48.28 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.1808 / WRfactor Rwork: 0.1581 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8864 / SU B: 1.728 / SU ML: 0.056 / SU R Cruickshank DPI: 0.0909 / SU Rfree: 0.0909 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1495 5 %RANDOM
Rwork0.1654 ---
all0.1668 29775 --
obs0.1668 29775 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: 500 Å2 / Biso mean: 26.3871 Å2 / Biso min: 10.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2--0.61 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.759→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 27 159 1936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221814
X-RAY DIFFRACTIONr_bond_other_d0.0010.021183
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9532467
X-RAY DIFFRACTIONr_angle_other_deg0.93532887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2185220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49224.69983
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.07215295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.239158
X-RAY DIFFRACTIONr_chiral_restr0.0860.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022007
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
X-RAY DIFFRACTIONr_mcbond_it6.8071.51103
X-RAY DIFFRACTIONr_mcbond_other1.1991.5448
X-RAY DIFFRACTIONr_mcangle_it8.52121766
X-RAY DIFFRACTIONr_scbond_it36.9643711
X-RAY DIFFRACTIONr_scangle_it35.5814.5701
LS refinement shellResolution: 1.759→1.805 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 117 -
Rwork0.241 2049 -
all-2166 -
obs--100 %

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