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- PDB-2y1t: Bacillus subtilis prophage dUTPase in complex with dUDP -

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Basic information

Entry
Database: PDB / ID: 2y1t
TitleBacillus subtilis prophage dUTPase in complex with dUDP
ComponentsSPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS
KeywordsHYDROLASE / SPB PROPHAGE / PHE-LID
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding / protein-containing complex / identical protein binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
DEOXYURIDINE-5'-DIPHOSPHATE / SPbeta prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsGarcia-Nafria, J. / Harkiolaki, M. / Persson, R. / Fogg, M.J. / Wilson, K.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: The Structure of Bacillus Subtilis Sp Beta Prophage Dutpase and its Complexes with Two Nucleotides
Authors: Garcia-Nafria, J. / Harkiolaki, M. / Persson, R. / Fogg, M.J. / Wilson, K.S.
History
DepositionDec 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 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

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Assembly

Deposited unit
A: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS
B: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS
C: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS
D: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS
E: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS
F: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,97611
Polymers97,0356
Non-polymers1,9415
Water9,134507
1
A: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS
B: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS
C: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2945
Polymers48,5183
Non-polymers7762
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9230 Å2
ΔGint-64.8 kcal/mol
Surface area17260 Å2
MethodPISA
2
D: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS
E: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS
F: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6826
Polymers48,5183
Non-polymers1,1643
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9880 Å2
ΔGint-66.9 kcal/mol
Surface area17070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.515, 99.338, 99.306
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS / DEOXYURIDINE TRIPHOSPHATE NUCLEOTIDOHYDROLASE / DUTPASE / DUTP PYROPHOSPHATASE


Mass: 16172.509 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: O34919, dUTP diphosphatase
#2: Chemical
ChemComp-DUD / DEOXYURIDINE-5'-DIPHOSPHATE


Mass: 388.162 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H14N2O11P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.27 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1M HEPES BUFFER PH 7.5, 10% (V/V) PEG 8000, 8% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 10, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.555
11-L, -H, K20.408
11K, -L, -H30.037
ReflectionResolution: 1.9→20 Å / Num. obs: 78511 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.4
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.1 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.6.0086refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CHAIN A OF PDB ENTRY 2XX6

2xx6


Resolution: 1.89→70.31 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 4.374 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.166 3929 5 %RANDOM
Rwork0.14 ---
obs0.142 74316 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.95 Å2
Baniso -1Baniso -2Baniso -3
1--3.73 Å20 Å20 Å2
2--3.45 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.89→70.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6215 0 120 507 6842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0226441
X-RAY DIFFRACTIONr_bond_other_d0.0010.024510
X-RAY DIFFRACTIONr_angle_refined_deg2.3231.9918706
X-RAY DIFFRACTIONr_angle_other_deg1.179310962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.085770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5124.286294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.912151182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5341542
X-RAY DIFFRACTIONr_chiral_restr0.1410.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0216948
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021290
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_it1.3531.53819
X-RAY DIFFRACTIONr_mcbond_other0.4291.51544
X-RAY DIFFRACTIONr_mcangle_it2.21526180
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.44332635
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.094.52536
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: 1.89→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 268 -
Rwork0.154 5022 -
obs--91.38 %
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)
10.65370.09660.14850.2759-0.03370.33210.0429-0.0181-0.1087-0.0328-0.00810.04160.02580.0251-0.03480.01390.0044-0.00580.00650.01110.1069-9.2323-7.7744-43.0119
20.23070.052-0.03820.5849-0.12310.32450.00490.0187-0.037-0.0699-0.00210.0457-0.04980.0519-0.00280.041-0.0078-0.00710.0208-0.01090.0529-4.81169.6472-54.6714
30.3874-0.03980.20690.2460.04010.58930.0217-0.0147-0.03660.0132-0.0352-0.0403-0.06170.0830.01350.0183-0.02130.00020.05420.01450.06067.21434.87-38.3977
40.5603-0.0067-0.02210.37650.1010.4809-0.0297-0.0160.0128-0.0193-0.01340.01150.0372-0.08140.04320.0073-0.0044-0.00420.058-0.0050.0567-4.956342.6917-39.982
50.61630.181-0.13620.36460.00090.15720.0338-0.00410.0767-0.0635-0.0123-0.05560-0.0252-0.02150.03030.0060.00920.0109-0.00520.100612.052154.3611-44.7394
60.53720.0196-0.13890.69410.24380.2424-0.06830.0971-0.0242-0.12560.0566-0.06280.0022-0.07040.01180.0576-0.03070.03310.0617-0.00420.05836.816638.0581-57.1892
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 128
2X-RAY DIFFRACTION2B1 - 143
3X-RAY DIFFRACTION3C1 - 143
4X-RAY DIFFRACTION4D1 - 143
5X-RAY DIFFRACTION5E1 - 144
6X-RAY DIFFRACTION6F1 - 128

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