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- PDB-2yay: The Crystal Structure of Leishmania major dUTPase in complex with... -

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Basic information

Entry
Database: PDB / ID: 2yay
TitleThe Crystal Structure of Leishmania major dUTPase in complex with substrate analogue dUpNpp
ComponentsDUTPASE
KeywordsHYDROLASE / LEISHMANIASIS
Function / homology
Function and homology information


dUTP diphosphatase / dUTP diphosphatase activity / nucleoplasm / metal ion binding
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
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / Putative deoxyuridine triphosphatase
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsHemsworth, G.R. / Moroz, O.V. / Fogg, M.J. / Scott, B. / Bosch-Navarrete, C. / Gonzalez-Pacanowska, D. / Wilson, K.S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The Crystal Structure of the Leishmania Major Deoxyuridine Triphosphate Nucleotidohydrolase in Complex with Nucleotide Analogues, Dump, and Deoxyuridine.
Authors: Hemsworth, G.R. / Moroz, O.V. / Fogg, M.J. / Scott, B. / Bosch-Navarrete, C. / Gonzalez-Pacanowska, D. / Wilson, K.S.
History
DepositionFeb 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_conn.ptnr2_label_seq_id / _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: DUTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1574
Polymers30,6101
Non-polymers5473
Water99155
1
A: DUTPASE
hetero molecules

A: DUTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3148
Polymers61,2202
Non-polymers1,0956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area5530 Å2
ΔGint-78.8 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.830, 86.830, 145.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein DUTPASE / DEOXYURIDINE TRIPHOSPHATASE (DUTP DIPHOSPHATASE) / DEOXYURIDINE TRIPHOSPHATE NUCLEOTIDOHYDROLASE


Mass: 30609.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Strain: 252 / Plasmid: PET-YSBLLIC3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15826, dUTP diphosphatase
#2: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.55 Å3/Da / Density % sol: 51.79 % / Description: NONE
Crystal growDetails: 0.2 M CACL2, 0.1 M MES PH 6.0, 20% PEG 6000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→43.4 Å / Num. obs: 25978 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 17.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 30.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.6 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CJE

2cje


Resolution: 1.86→28.42 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.253 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24852 1353 5 %RANDOM
Rwork0.21436 ---
obs0.21611 25688 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.799 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.86→28.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 30 55 2028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222020
X-RAY DIFFRACTIONr_bond_other_d0.0010.021266
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9522768
X-RAY DIFFRACTIONr_angle_other_deg0.99433084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6225256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42124.11885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74815284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.958159
X-RAY DIFFRACTIONr_chiral_restr0.0910.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212283
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02422
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_it28.4061.51286
X-RAY DIFFRACTIONr_mcbond_other2.5611.5511
X-RAY DIFFRACTIONr_mcangle_it25.3122039
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it26.4283734
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it19.5424.5729
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.861→1.909 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 88 -
Rwork0.38 1886 -
obs--98.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.5652-2.3775-0.05913.7999-1.24685.0247-0.419-0.3641-0.23080.28650.1332-0.26960.3490.58920.28570.09760.0165-0.04580.22280.14820.1658-1.84629.8091.152
24.3982-2.14920.8373.847-1.40691.8895-0.2586-0.30560.62150.7053-0.0439-0.4408-0.47470.13770.30240.1988-0.1054-0.12330.18450.05940.1549-8.746.345-2.458
35.4355-0.9445-0.25465.61470.23785.1303-0.172-0.634-0.5940.48610.28890.46570.0384-0.1718-0.1170.08240.00790.05780.22090.19240.2038-17.04927.7387
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 44
2X-RAY DIFFRACTION2A45 - 170
3X-RAY DIFFRACTION3A171 - 250

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