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- PDB-2yaz: The Crystal Structure of Leishmania major dUTPase in complex dUMP -

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Basic information

Entry
Database: PDB / ID: 2yaz
TitleThe Crystal Structure of Leishmania major dUTPase in complex dUMP
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'-MONOPHOSPHATE / Putative deoxyuridine triphosphatase
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
B: DUTPASE
D: DUTPASE
E: DUTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,12915
Polymers122,4394
Non-polymers1,69011
Water63135
1
A: DUTPASE
B: DUTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0527
Polymers61,2202
Non-polymers8335
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-61 kcal/mol
Surface area21990 Å2
MethodPISA
2
D: DUTPASE
E: DUTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0778
Polymers61,2202
Non-polymers8576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-67 kcal/mol
Surface area21340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.110, 109.110, 309.311
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 30609.850 Da / Num. of mol.: 4
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-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#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


Mass: 18.015 Da / Num. of mol.: 35 / 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: 4.29 Å3/Da / Density % sol: 71.32 % / Description: NONE
Crystal growDetails: 0.1 M NACL, 0.1 M BIS-TRIS PH 6.5, 1.5 M (NH4)2 SO4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.4→54.6 Å / Num. obs: 84915 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 14.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 16.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

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

2cje


Resolution: 2.4→103.1 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / SU B: 12.142 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22532 4239 5 %RANDOM
Rwork0.20268 ---
obs0.20383 80604 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.832 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å20 Å2
2--0.07 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.4→103.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7979 0 103 35 8117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228271
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.95311315
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.37451030
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09324.72375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.122151223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1571535
X-RAY DIFFRACTIONr_chiral_restr0.0930.21275
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216343
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.21.55172
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.68728258
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.79133099
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.4824.53057
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: 2.396→2.458 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 278 -
Rwork0.314 5867 -
obs--99.74 %
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)
12.22360.45970.25822.64920.04393.26530.1481-0.2454-0.18190.4757-0.14140.05040.0401-0.0494-0.00660.2528-0.161-0.03480.1370.01780.1577-27.00943.806-5.597
26.4610.666-2.53543.3879-2.33895.6530.0698-0.1749-0.68790.1428-0.1527-0.0160.66940.20790.08290.3708-0.0675-0.0410.14150.00180.3618-22.00826.774-15.529
32.01340.24980.34284.2758-0.60692.79110.03230.00350.07930.2172-0.0537-0.2418-0.2550.20550.02130.2974-0.1946-0.0570.18490.00150.2013-12.85962.868-6.594
45.366-2.3391.86467.93691.17696.6831-0.16930.9676-0.1598-0.40020.0102-0.71240.02680.79890.15910.5168-0.33610.04810.49620.07750.4154-3.70873.472-20.216
52.712-0.4762-0.41181.6172-0.00313.96490.0560.6456-0.1401-0.1287-0.076-0.17880.2140.22090.020.0346-0.0145-0.02020.4864-0.04920.219-24.52541.456-46.63
63.64621.0969-2.26957.2818-1.13735.5753-0.3260.4018-0.6755-0.28790.0613-0.38860.80150.45660.26480.18060.1022-0.01410.5748-0.10190.4753-10.09428.984-40.962
73.934-0.3926-0.25072.21610.0493.86840.10150.3956-0.2207-0.0604-0.03520.1270.1145-0.3021-0.06640.0227-0.0519-0.05040.4871-0.05350.2553-48.32840.776-46.701
84.9512-2.97430.53056.27151.52757.67940.2206-0.3273-0.92220.6111-0.00280.12430.9997-0.5631-0.21790.2328-0.2139-0.03460.75430.05020.5748-62.25633.032-35.056
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 175
2X-RAY DIFFRACTION2A176 - 264
3X-RAY DIFFRACTION3B2 - 195
4X-RAY DIFFRACTION4B196 - 264
5X-RAY DIFFRACTION5D8 - 195
6X-RAY DIFFRACTION6D196 - 264
7X-RAY DIFFRACTION7E8 - 195
8X-RAY DIFFRACTION8E196 - 264

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