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- PDB-4wrk: The 3D structure of D95N mutant DUTPase from phage phi11 of S. au... -

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Basic information

Entry
Database: PDB / ID: 4wrk
TitleThe 3D structure of D95N mutant DUTPase from phage phi11 of S. aureus reveals the molecular details for the coordination of a structural Mg(II) ion
ComponentsDUTPase
KeywordsHYDROLASE / Magnesium coordination mutant / jelly-roll
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 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / dUTP diphosphatase
Similarity search - Component
Biological speciesStaphylococcus phage phi11 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBendes, A.A. / Leveles, I. / Vertessy, B.G.
Funding support Hungary, 6items
OrganizationGrant numberCountry
ungarian Scientific Research Fund OTKANK 84008 Hungary
ungarian Scientific Research Fund OTKAK109486 Hungary
Baross Program of the New Hungary Development Plan3DSTRUCT, MFB-00266/2010 REG-KM-09-1-2009-005 Hungary
Hungarian Academy of SciencesTTK IF-28/201 Hungary
Hungarian Academy of SciencesMedinProt program Hungary
European Union283570
CitationJournal: To Be Published
Title: The 3D structure of D95N mutant DUTPase from phage phi11 of S. aureus reveals the molecular details for the coordination of a structural Mg(II) ion
Authors: Bendes, A.A. / Leveles, I. / Vertessy, B.G.
History
DepositionOct 24, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 2.0Jan 10, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.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
C: DUTPase
D: DUTPase
E: DUTPase
F: DUTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,26818
Polymers110,3206
Non-polymers2,94912
Water1,820101
1
A: DUTPase
B: DUTPase
C: DUTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6349
Polymers55,1603
Non-polymers1,4746
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12090 Å2
ΔGint-87 kcal/mol
Surface area19490 Å2
MethodPISA
2
D: DUTPase
E: DUTPase
F: DUTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6349
Polymers55,1603
Non-polymers1,4746
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12030 Å2
ΔGint-88 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.420, 108.420, 167.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
DUTPase


Mass: 18386.600 Da / Num. of mol.: 6 / Mutation: D95N
Source method: isolated from a genetically manipulated source
Details: D95N MUTANT DUTPASE FROM PHAGE PHI11 OF S.AUREUS / Source: (gene. exp.) Staphylococcus phage phi11 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8SDV3
#2: Chemical
ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: 0.1M sodium acetate, 15 - 41.5% MPD, 0.02M calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 15, 2014
RadiationMonochromator: Confocal collimator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→19.57 Å / Num. obs: 22585 / % possible obs: 100 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.208 / Net I/σ(I): 8.6
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.358 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GV8

4gv8


Resolution: 2.9→19.57 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 1136 5.03 %
Rwork0.2085 --
obs0.211 22581 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.1 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6883 0 174 101 7158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067167
X-RAY DIFFRACTIONf_angle_d0.9329802
X-RAY DIFFRACTIONf_dihedral_angle_d11.7182493
X-RAY DIFFRACTIONf_chiral_restr0.0381159
X-RAY DIFFRACTIONf_plane_restr0.0051250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.03160.35981610.2982633X-RAY DIFFRACTION100
3.0316-3.19070.3571270.2822663X-RAY DIFFRACTION100
3.1907-3.38970.2791330.24492638X-RAY DIFFRACTION100
3.3897-3.64990.27321340.22762661X-RAY DIFFRACTION100
3.6499-4.01430.26511490.20392663X-RAY DIFFRACTION100
4.0143-4.58860.20681400.1732672X-RAY DIFFRACTION100
4.5886-5.75670.26441410.17682715X-RAY DIFFRACTION99
5.7567-19.5730.20851510.18852800X-RAY DIFFRACTION98
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)
10.5661-0.56670.01180.85210.53951.0757-0.08780.18040.3129-0.03070.1065-0.06970.1685-0.049-00.1765-0.00610.01910.19290.04790.2321-12.6115-28.5201-32.1269
20.0018-0.2644-0.29110.02420.0215-0.03120.8503-0.64210.49770.0487-0.56550.1695-0.28790.23600.18080.06130.02540.34640.01780.4709-29.7472-21.6103-20.1355
30.21580.64760.05280.3185-0.47010.0928-0.14240.1984-0.2168-0.12920.2244-0.1342-0.0850.027400.20330.0669-0.03910.27440.06660.19025.028-36.8085-26.4966
40.64020.2403-0.40680.81590.40351.30220.0208-0.06990.16520.08220.03360.10080.04240.249900.23570.01540.01180.1840.00120.23010.7292-19.1794-14.2698
50.2358-0.7180.1050.3050.42030.5655-0.0766-0.2409-0.3467-0.1434-0.1508-0.1664-0.09950.305900.22570.03450.07350.2855-0.0760.2837-11.326-23.10963.9527
6-0.0066-0.56040.57840.4713-0.07990.07190.03080.21520.01080.05930.1170.09420.22260.220200.2505-0.06640.04410.30560.01950.2198-1.432-27.3124-30.8466
71.41250.01130.1094-0.14410.3162-0.1851-0.05040.04310.0121-0.10810.1049-0.09030.1216-0.0568-00.21320.01410.00010.2401-00.2202-0.7586-43.2889-16.9908
8-0.04210.4686-0.14140.2962-0.27990.35070.19110.21730.0594-0.04390.08350.08810.0993-0.4099-00.3318-0.07160.03120.38530.05360.2516-20.846-48.3681-9.0607
90.3919-0.24710.17620.0110.30960.9081-0.16070.0077-0.0418-0.20070.1233-0.0908-0.03310.0503-00.13190.0212-0.00850.1266-0.03260.22436.3998-26.4612-21.6598
101.1389-0.285-0.46131.0684-0.15211.5108-0.1195-0.0706-0.19730.0463-0.1007-0.04310.1609-0.2136-00.2312-0.04020.04610.20820.01050.1823-36.2717-9.3241-54.7581
110.01350.0113-0.26310.27750.26150.16680.01020.1337-0.15160.10430.00220.06770.01880.031800.40420.0522-0.01350.3604-0.06070.3776-40.755112.3526-48.0077
120.2920.28010.4524-0.03960.08081.03690.09081.1960.2647-0.59640.33490.23791.5498-1.52410-0.30140.32350.191-0.3932-0.3510.0206-24.4889-13.1289-58.46
131.0530.58540.63360.72420.46890.9268-0.09430.21280.0077-0.0620.0675-0.05810.0130.0775-00.23050.0231-0.01810.21450.01010.1699-22.95421.5908-72.0971
140.2791-0.02040.28640.41760.0170.0585-0.32540.53320.93850.29250.141-0.57020.76070.961400.0958-0.3476-0.0279-0.6078-0.01670.5683-15.056219.6408-62.0356
150.2805-0.43830.46530.25640.57590.49190.12290.0907-0.0967-0.5311-0.5017-0.14680.56470.6186-00.3585-0.108-0.02-0.0277-0.14240.2343-29.6791-12.096-64.5232
161.2192-0.58970.09990.9623-0.24911.46590.09410.05860.02740.1011-0.0175-0.07780.1902-0.038900.2367-0.0125-0.01260.1243-0.01160.1524-11.8115-10.3967-54.3088
170.07580.2160.23630.31560.19460.24110.1506-0.29260.0157-0.2921-0.3625-0.10860.205-0.1323-00.4014-0.0417-0.06420.2413-0.01260.2533-13.78493.1308-36.7113
180.73060.2308-1.1010.68360.3030.3772-0.1150.1973-0.1639-0.0740.12420.08020.1871-0.080500.2956-0.00590.02150.1735-0.02580.2206-21.1027-9.5946-69.8486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 159 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 94 )
5X-RAY DIFFRACTION5chain 'B' and (resid 95 through 129 )
6X-RAY DIFFRACTION6chain 'B' and (resid 130 through 164 )
7X-RAY DIFFRACTION7chain 'C' and (resid 3 through 94 )
8X-RAY DIFFRACTION8chain 'C' and (resid 95 through 129 )
9X-RAY DIFFRACTION9chain 'C' and (resid 130 through 155 )
10X-RAY DIFFRACTION10chain 'D' and (resid 3 through 94 )
11X-RAY DIFFRACTION11chain 'D' and (resid 95 through 125 )
12X-RAY DIFFRACTION12chain 'D' and (resid 126 through 155 )
13X-RAY DIFFRACTION13chain 'E' and (resid 3 through 94 )
14X-RAY DIFFRACTION14chain 'E' and (resid 95 through 129 )
15X-RAY DIFFRACTION15chain 'E' and (resid 130 through 164 )
16X-RAY DIFFRACTION16chain 'F' and (resid 2 through 94 )
17X-RAY DIFFRACTION17chain 'F' and (resid 95 through 129 )
18X-RAY DIFFRACTION18chain 'F' and (resid 130 through 164 )

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