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- PDB-3h6x: Crystal structure of dUTPase from Streptococcus mutans -

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Basic information

Entry
Database: PDB / ID: 3h6x
TitleCrystal structure of dUTPase from Streptococcus mutans
ComponentsdUTPase
KeywordsHYDROLASE / jelly-roll beta-barrel
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
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsLi, G.L. / Wang, K.T. / Liu, X. / Li, L.F. / Su, X.D.
CitationJournal: To be Published
Title: Structure and activity analysis of dUTP nucleotidohydrolase from Streptococcus mutans
Authors: Li, G.L. / Wang, K.T. / Liu, X. / Li, L.F. / Su, X.D.
History
DepositionApr 24, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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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


Theoretical massNumber of molelcules
Total (without water)49,1753
Polymers49,1753
Non-polymers00
Water12,394688
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-42 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.780, 53.520, 93.140
Angle α, β, γ (deg.)90.00, 113.91, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-420-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 4:132 )A4 - 132
211chain B and (resseq 4:132 )B4 - 132
311chain C and (resseq 4:132 )C4 - 132

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Components

#1: Protein dUTPase


Mass: 16391.641 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: dut / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8DVY3, dUTP diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 2.07 Å3/Da / Density % sol: 40.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M MgCl2, 25% polyethylene glycol(PEG)3350, 0.1M Tris-HCl(pH 8.5), pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.9787 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 43830 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 11.33 Å2 / Rsym value: 0.047 / Net I/σ(I): 15.25
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 8.97 / Num. unique all: 7142 / Rsym value: 0.123 / % possible all: 96.1

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Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→19.941 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.7 / FOM work R set: 0.885 / SU B: 1.831 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.09 / Phase error: 18.8 / Stereochemistry target values: MLHL / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 1994 4.62 %RANDOM
Rwork0.1833 41170 --
obs0.1843 43164 97.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.132 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 50.15 Å2 / Biso mean: 14.753 Å2 / Biso min: 1.54 Å2
Baniso -1Baniso -2Baniso -3
1--1.128 Å20 Å2-1.201 Å2
2---0.474 Å2-0 Å2
3---1.602 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 0 688 3696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093059
X-RAY DIFFRACTIONf_angle_d1.2594144
X-RAY DIFFRACTIONf_dihedral_angle_d16.0861113
X-RAY DIFFRACTIONf_chiral_restr0.112473
X-RAY DIFFRACTIONf_plane_restr0.006543
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1002X-RAY DIFFRACTIONPOSITIONAL0.072
12B1002X-RAY DIFFRACTIONPOSITIONAL0.072
13C995X-RAY DIFFRACTIONPOSITIONAL0.053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74250.231210.19482577X-RAY DIFFRACTION86
1.7425-1.78960.21471550.17542928X-RAY DIFFRACTION98
1.7896-1.84220.22361420.17912911X-RAY DIFFRACTION98
1.8422-1.90160.2031320.1812939X-RAY DIFFRACTION98
1.9016-1.96950.2051420.18252924X-RAY DIFFRACTION99
1.9695-2.04830.2341480.17712975X-RAY DIFFRACTION99
2.0483-2.14140.19621430.17642979X-RAY DIFFRACTION99
2.1414-2.25420.19361420.19062976X-RAY DIFFRACTION99
2.2542-2.39520.211430.19272940X-RAY DIFFRACTION99
2.3952-2.57980.2041470.18472990X-RAY DIFFRACTION99
2.5798-2.83870.23631360.19723007X-RAY DIFFRACTION99
2.8387-3.2480.18731570.1822991X-RAY DIFFRACTION99
3.248-4.08630.181420.16343007X-RAY DIFFRACTION99
4.0863-19.94240.18641440.16933026X-RAY DIFFRACTION97

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