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- PDB-2yb0: The Crystal Structure of Leishmania major dUTPase in complex deox... -

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Basic information

Entry
Database: PDB / ID: 2yb0
TitleThe Crystal Structure of Leishmania major dUTPase in complex deoxyuridine
ComponentsDUTPASE
KeywordsHYDROLASE
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 / Putative deoxyuridine triphosphatase
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 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 / 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 / _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)124,21717
Polymers122,4394
Non-polymers1,77713
Water1,74797
1
A: DUTPASE
B: DUTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1569
Polymers61,2202
Non-polymers9377
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-106.9 kcal/mol
Surface area21770 Å2
MethodPISA
2
D: DUTPASE
E: DUTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0608
Polymers61,2202
Non-polymers8416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-82 kcal/mol
Surface area21680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.186, 109.186, 308.882
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 TRIPHOSPHATE NUCLEOTIDOHYDROLASE / DEOXYURIDINE TRIPHOSPHATASE / DUTP DIPHOSPHATASE


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-DUR / 2'-DEOXYURIDINE


Mass: 228.202 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H12N2O5
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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)2SO4

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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: 2.28→60.8 Å / Num. obs: 98557 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 13.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.4
Reflection shellResolution: 2.28→2.4 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 3 / % possible all: 99.8

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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: 2.28→54.59 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.849 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4921 5 %RANDOM
Rwork0.21 ---
obs0.211 93350 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.18 Å20 Å2
2--0.35 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.28→54.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8004 0 109 97 8210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228300
X-RAY DIFFRACTIONr_bond_other_d0.0010.025247
X-RAY DIFFRACTIONr_angle_refined_deg1.251.95211349
X-RAY DIFFRACTIONr_angle_other_deg0.906312799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.31751036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97524.667375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.449151222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0411536
X-RAY DIFFRACTIONr_chiral_restr0.0780.21276
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219356
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021704
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_it3.0751.55203
X-RAY DIFFRACTIONr_mcbond_other1.1891.52068
X-RAY DIFFRACTIONr_mcangle_it4.38228297
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.75533097
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.1594.53052
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: 2.28→2.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 358 -
Rwork0.364 6774 -
obs--100 %
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)
11.78760.16590.10282.38160.16572.96370.1116-0.219-0.23320.448-0.10760.02210.1274-0.0621-0.00390.2385-0.1477-0.05360.12880.03560.1764-25.60942.408-6.53
26.1520.2546-2.28742.3406-2.07174.98450.0163-0.1831-0.80780.1174-0.02550.27580.6312-0.03680.00920.3628-0.0771-0.05230.13340.01090.3952-23.94125.492-15.757
31.9050.04080.3473.7729-0.4962.28050.0317-0.00650.0820.3032-0.0275-0.1899-0.28910.1667-0.00420.2684-0.1755-0.05960.15750.00620.1773-12.76763.028-6.541
43.9754-2.1151.92587.61431.29225.8907-0.08810.7604-0.0419-0.31480.0206-0.7046-0.03960.64370.06760.4483-0.32260.02090.44350.08070.3424-3.6273.383-20.319
52.634-0.3969-0.63811.18670.40964.22740.00020.6065-0.2892-0.0923-0.021-0.18480.36090.27680.02080.0697-0.0016-0.03240.393-0.09790.2453-24.5437.787-47.151
63.6395-1.32490.18012.2638-0.24453.31270.03520.506-0.3186-0.0968-0.0757-0.15340.43860.2940.04050.0721-0.02130.00970.3865-0.07760.2363-18.83638.548-43.663
74.046-0.2858-0.21071.98870.12773.60.04580.3703-0.2318-0.07620.00630.09330.1142-0.2729-0.05210.0222-0.0478-0.04740.4176-0.06670.2321-48.28140.749-46.612
85.3391-2.88741.14326.391.29666.70490.2221-0.36-0.92390.461-0.13410.17110.7544-0.6092-0.08810.1666-0.1978-0.03090.69820.07970.515-62.58433.363-35.096
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 196
2X-RAY DIFFRACTION2A197 - 264
3X-RAY DIFFRACTION3B2 - 195
4X-RAY DIFFRACTION4B196 - 264
5X-RAY DIFFRACTION5D8 - 96
6X-RAY DIFFRACTION6D97 - 262
7X-RAY DIFFRACTION7E8 - 195
8X-RAY DIFFRACTION8E196 - 264

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