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- PDB-4aoo: B. subtilis dUTPase YncF in complex with dU PPi and Mg in H32 -

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Basic information

Entry
Database: PDB / ID: 4aoo
TitleB. subtilis dUTPase YncF in complex with dU PPi and Mg in H32
ComponentsPROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF
KeywordsHYDROLASE
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion 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 / PHOSPHATE ION / PYROPHOSPHATE 2- / Deoxyuridine 5'-triphosphate nucleotidohydrolase YncF
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGarcia-Nafria, J. / Timm, 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 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 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.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.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.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_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: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF
B: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF
C: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF
D: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,53617
Polymers65,7274
Non-polymers1,80913
Water4,053225
1
B: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF
C: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF
D: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,67613
Polymers49,2953
Non-polymers1,38010
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16490 Å2
ΔGint-83 kcal/mol
Surface area15880 Å2
MethodPISA
2
A: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF
hetero molecules

A: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF
hetero molecules

A: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,58112
Polymers49,2953
Non-polymers1,2859
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area16430 Å2
ΔGint-79.5 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.628, 146.628, 144.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2013-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF / DUTPASE / DUTP PYROPHOSPHATASE


Mass: 16431.760 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O31801, dUTP diphosphatase

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Non-polymers , 5 types, 238 molecules

#2: Chemical
ChemComp-DUR / 2'-DEOXYURIDINE


Mass: 228.202 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H12N2O5
#3: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.08 Å3/Da / Density % sol: 40.91 % / Description: NONE
Crystal growpH: 6.5
Details: 30% MPD, 0.1 M SODIUM CACODYLATE PH 6.5, 0.2 M MAGNESIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.3→70 Å / Num. obs: 26728 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 11.3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 22.64
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 11 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XCD

2xcd


Resolution: 2.3→95.47 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.926 / SU B: 12.082 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21861 1343 5 %RANDOM
Rwork0.16265 ---
obs0.16553 25311 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.698 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.3→95.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4551 0 109 225 4885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.024744
X-RAY DIFFRACTIONr_bond_other_d0.0060.023294
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.9876401
X-RAY DIFFRACTIONr_angle_other_deg0.91538036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87424.562217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26615873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8331528
X-RAY DIFFRACTIONr_chiral_restr0.0960.2689
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025148
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02940
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 103 -
Rwork0.216 1762 -
obs--99.63 %
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)
10.78760.014-0.0970.793-0.00850.11870.0514-0.08840.00910.1398-0.0547-0.1448-0.02870.02930.00330.1363-0.0102-0.03880.14180.00480.02859.2807-0.706243.6434
20.5235-0.30360.23320.8605-0.17110.8422-0.02450.0076-0.0919-0.02060.03880.2356-0.0054-0.0787-0.01420.0299-0.0090.01760.05920.0240.143932.821524.966255.5555
30.485-0.39550.14191.13990.15930.6193-0.1443-0.0839-0.02470.27660.16170.2056-0.0282-0.0016-0.01740.11970.02390.06880.09160.05080.082237.987926.573170.6123
40.3901-0.34890.10770.9490.25540.7828-0.0167-0.0567-0.10920.08960.05010.15320.14120.0289-0.03340.1004-0.01040.03520.05240.04420.105642.043913.46362.0053
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 144
2X-RAY DIFFRACTION2B3 - 144
3X-RAY DIFFRACTION3C3 - 144
4X-RAY DIFFRACTION4D3 - 144

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