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- PDB-4ao5: B. subtilis prophage dUTPase YosS in complex with dUMP -

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Basic information

Entry
Database: PDB / ID: 4ao5
TitleB. subtilis prophage dUTPase YosS in complex with dUMP
ComponentsSPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEO TIDOHYDROLASE YOSS
KeywordsHYDROLASE / HOMOTRIMERIC DUTPASES / 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
2'-DEOXYURIDINE 5'-MONOPHOSPHATE / SPbeta prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGarcia-Nafria, J. / Harrison, C. / Turkenburg, J.P. / Wilson, K.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Tying Down the Arm in Bacillus Dutpase: Structure and Mechanism
Authors: Garcia-Nafria, J. / Timm, J. / Harrison, C. / Turkenburg, J.P. / Wilson, K.S.
History
DepositionMar 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references / Structure summary
Revision 1.2Aug 7, 2013Group: Database references
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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _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 NUCLEO TIDOHYDROLASE YOSS
B: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEO TIDOHYDROLASE YOSS
C: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEO TIDOHYDROLASE YOSS
D: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEO TIDOHYDROLASE YOSS
E: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEO TIDOHYDROLASE YOSS
F: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEO TIDOHYDROLASE YOSS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,35117
Polymers98,3876
Non-polymers1,96411
Water20,4831137
1
A: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEO TIDOHYDROLASE YOSS
B: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEO TIDOHYDROLASE YOSS
C: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEO TIDOHYDROLASE YOSS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1879
Polymers49,1933
Non-polymers9946
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9160 Å2
ΔGint-89.5 kcal/mol
Surface area17090 Å2
MethodPISA
2
D: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEO TIDOHYDROLASE YOSS
E: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEO TIDOHYDROLASE YOSS
F: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEO TIDOHYDROLASE YOSS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1648
Polymers49,1933
Non-polymers9715
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-94.2 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.820, 100.010, 99.510
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 NUCLEO TIDOHYDROLASE YOSS / DUTPASE / DUTP PYROPHOSPHATASE


Mass: 16397.756 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) / References: UniProt: O34919, dUTP diphosphatase
#2: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1137 / 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: 2.2 Å3/Da / Density % sol: 44.17 % / Description: NONE
Crystal growpH: 7.5
Details: 14% PEG 3350, 0.1 M SODIUM MALONATE, 0.1 M, BIS-TRIS PROPANE PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.6→28.8 Å / Num. obs: 131522 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XCD

2xcd


Resolution: 1.6→70.65 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.92 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21365 6577 5 %RANDOM
Rwork0.1503 ---
obs0.15347 123669 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.005 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.44 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.6→70.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6273 0 125 1137 7535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.026672
X-RAY DIFFRACTIONr_bond_other_d0.0010.024695
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.9889029
X-RAY DIFFRACTIONr_angle_other_deg0.841311496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0815817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5224.647312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.532151281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0071540
X-RAY DIFFRACTIONr_chiral_restr0.0820.2975
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027244
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021334
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.71611367
X-RAY DIFFRACTIONr_sphericity_free33.8175296
X-RAY DIFFRACTIONr_sphericity_bonded12.43912076
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 469 -
Rwork0.216 8710 -
obs--99.84 %

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