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- PDB-2baz: Structure of YosS, a putative dUTPase from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 2baz
TitleStructure of YosS, a putative dUTPase from Bacillus subtilis
Componentshypothetical protein BSU20020Hypothesis
KeywordsUNKNOWN FUNCTION / homotrimer / beta barrel
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
SPbeta prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsLiang, Y.-H. / Wang, J. / Su, X.-D.
CitationJournal: To be Published
Title: Structure of YosS, a putative dUTPase from Bacillus subtilis
Authors: Wang, J. / Liang, Y.-H. / Su, X.-D.
History
DepositionOct 16, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein BSU20020
B: hypothetical protein BSU20020
C: hypothetical protein BSU20020


Theoretical massNumber of molelcules
Total (without water)48,5183
Polymers48,5183
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-66 kcal/mol
Surface area16430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.500, 116.500, 56.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsThe asymmetric unit contains one biological unit which is a homotrimer.

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Components

#1: Protein hypothetical protein BSU20020 / Hypothesis / YosS


Mass: 16172.509 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: O34919
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 3.97 Å3/Da / Density % sol: 69.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.0M (NH4)2SO4, 0.1M Na Citrate, 0.2M K/Na Tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9803, 0.981, 1.1
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 28, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98031
20.9811
31.11
Reflection
IDNumberRmerge(I) obsΧ2D res high (Å)D res low (Å)% possible obs
1340100.0872.1232.32099.3
2338670.0741.8572.32098.9
3263580.0882.6922.52098.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
6.182097.910.0872.203
4.936.189910.0664.476
4.324.9399.410.0623.645
3.934.3298.810.0653.672
3.653.9393.810.083.663
3.433.6598.610.0783.006
3.263.4399.810.0843.018
3.123.2699.810.0862.347
33.1299.910.0982.494
2.9399.910.1051.898
2.812.910010.1171.526
2.732.8110010.1351.594
2.652.7310010.151.485
2.592.6599.910.1671.408
2.532.5999.910.1671.351
2.482.5399.910.1811.224
2.432.4899.910.2021.188
2.382.4399.810.2271.052
2.342.3899.910.2510.991
2.32.3410010.270.959
6.182096.720.0661.483
4.936.1898.420.0573.503
4.324.9398.720.0563.187
3.934.3297.520.0593.227
3.653.9390.720.0763.429
3.433.6597.420.0672.485
3.263.4399.720.0712.546
3.123.2699.920.0762.107
33.1299.820.0812.098
2.9399.720.0861.644
2.812.999.920.0981.314
2.732.8110020.1131.497
2.652.7310020.121.319
2.592.6510020.1381.358
2.532.5910020.1351.25
2.482.5399.920.1451.159
2.432.4810020.1661.155
2.382.4310020.1851.032
2.342.3810020.2020.977
2.32.3499.920.2190.973
6.72096.930.0891.748
5.356.798.530.0775.162
4.695.3598.230.0694.014
4.264.6998.630.0714.265
3.964.2698.230.0723.482
3.733.9695.930.083.535
3.543.7391.230.0954.455
3.393.5499.530.0883.313
3.263.3999.830.092.985
3.153.2699.430.0992.749
3.053.1599.830.1012.012
2.963.0599.830.1122.477
2.892.9699.930.1172.272
2.812.8999.830.132.416
2.752.8199.630.1381.975
2.692.7599.630.1461.854
2.642.6999.830.1561.823
2.592.6499.930.1671.55
2.542.5910030.1671.379
2.52.5499.830.1881.375
ReflectionResolution: 2.3→20 Å / Num. all: 34249 / Num. obs: 34010 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.087 / Χ2: 2.123
Reflection shellResolution: 2.3→2.34 Å / % possible obs: 100 % / Rmerge(I) obs: 0.27 / Num. measured obs: 1685 / Χ2: 0.959 / % possible all: 99.1

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.98034.56-6.7
13 wavelength20.9813.22-8.96
13 wavelength300.89-2.96
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se29.5950.0820.55701.103
2Se31.7630.4970.8680.2431.158
3Se49.5940.3830.7830.0011.38
4Se38.820.6180.6930.0391.257
5Se37.3940.5420.8270.0561.038
6Se37.2220.5370.7930.0170.923
7Se40.6790.5060.8180.0320.98
8Se40.7790.4390.7360.0671.319
9Se43.6340.60.7390.1641.364
10Se44.4230.160.520.1121.026
Phasing dmFOM : 0.61 / FOM acentric: 0.62 / FOM centric: 0.51 / Reflection: 26195 / Reflection acentric: 24667 / Reflection centric: 1528
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-19.9790.80.810.751120958162
4.5-7.10.790.80.6935893274315
3.6-4.50.710.710.5743414092249
3.1-3.60.630.640.4544744226248
2.7-3.10.540.550.3878707500370
2.5-2.70.430.430.2848014617184

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
RESOLVE2.03phasing
CNSrefinement
PDB_EXTRACT1.7data extraction
MAR345data collection
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1680 4.9 %Random
Rwork0.217 ---
all0.23 34186 --
obs0.225 33879 99.1 %-
Solvent computationBsol: 31.058 Å2
Displacement parametersBiso mean: 34.744 Å2
Baniso -1Baniso -2Baniso -3
1--1.744 Å20 Å20 Å2
2---1.744 Å20 Å2
3---3.487 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3043 0 0 148 3191
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param

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