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- PDB-2cje: THE CRYSTAL STRUCTURE OF A COMPLEX OF Leishmania major DUTPASE WI... -

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Basic information

Entry
Database: PDB / ID: 2cje
TitleTHE CRYSTAL STRUCTURE OF A COMPLEX OF Leishmania major DUTPASE WITH SUBSTRATE ANALOGUE DUPNHP
ComponentsDUTPASE
KeywordsHYDROLASE / PATHOGEN / ALL-ALPHA / DRUG TARGET
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-DIPHOSPHATE / Putative deoxyuridine triphosphatase
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsMoroz, O.V. / Fogg, M.J. / 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
DepositionMar 31, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 3, 2011Group: Database references / Derived calculations / Other
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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)30,8455
Polymers30,3851
Non-polymers4604
Water1,58588
1
A: DUTPASE
hetero molecules

A: DUTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,68910
Polymers60,7692
Non-polymers9208
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
MethodPQS
Unit cell
Length a, b, c (Å)87.866, 87.866, 146.531
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 / DUTP PYROPHOSPHATASE


Mass: 30384.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Plasmid: PET-YSBLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15826, 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.: 1 / Source method: obtained synthetically / Formula: C9H15N3O10P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 5.5
Details: 30% PEG 3350 MME, 0.2 M MGCL2, 0.1M BIS-TRIS PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.974
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 2.34→30 Å / Num. obs: 14713 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 13.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 28
Reflection shellResolution: 2.34→2.42 Å / Redundancy: 8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OGK

1ogk


Resolution: 2.34→76.03 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 12.812 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 737 5.1 %RANDOM
Rwork0.184 ---
obs0.187 13849 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.34→76.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 27 88 2115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222082
X-RAY DIFFRACTIONr_bond_other_d0.0010.021824
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9562846
X-RAY DIFFRACTIONr_angle_other_deg0.93934214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0745259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76524.74297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.21215315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7111510
X-RAY DIFFRACTIONr_chiral_restr0.0960.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022354
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02429
X-RAY DIFFRACTIONr_nbd_refined0.2180.2510
X-RAY DIFFRACTIONr_nbd_other0.1780.21857
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21009
X-RAY DIFFRACTIONr_nbtor_other0.0850.21115
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.272
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0150.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0920.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6691.51318
X-RAY DIFFRACTIONr_mcbond_other0.141.5518
X-RAY DIFFRACTIONr_mcangle_it1.09622071
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6653886
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5094.5775
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: 2.34→2.4 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 45 -
Rwork0.232 970 -
obs--97.04 %
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)
14.6009-1.4059-0.62842.4989-2.3428.2089-0.1347-0.4261-0.4120.18570.049-0.1450.39280.56980.0857-0.2826-0.0196-0.0078-0.06250.1795-0.1346-2.772130.87261.7794
22.8319-1.49870.82283.9022-1.59212.0802-0.2687-0.3160.30280.54290.0613-0.2222-0.4770.10680.2073-0.1322-0.0748-0.0693-0.10250.0832-0.214-8.499347.2182-2.2091
35.42930.8583-0.17826.21120.15935.5458-0.175-0.4419-0.43640.41230.16670.55970.2207-0.33180.0083-0.2398-0.00490.0723-0.00590.2549-0.0438-18.150528.86857.176
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 44
2X-RAY DIFFRACTION2A45 - 170
3X-RAY DIFFRACTION3A171 - 250

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