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- PDB-5xbn: crystal structure of Wss1 from saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 5xbn
Titlecrystal structure of Wss1 from saccharomyces cerevisiae
ComponentsWss1p
KeywordsHYDROLASE / protease
Function / homology:
Function and homology information
Biological speciesSaccharomyces cerevisiae FostersO (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.761 Å
AuthorsDong, Y.H. / Yang, X.Y. / Wang, W.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31600597 China
CitationJournal: To Be Published
Title: crystal structure of Wss1 from saccharomyces cerevisiae
Authors: Dong, Y.H. / Yang, X.Y.
History
DepositionMar 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Wss1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7232
Polymers17,6571
Non-polymers651
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-35 kcal/mol
Surface area7700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.195, 75.195, 43.739
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Wss1p


Mass: 17657.355 Da / Num. of mol.: 1 / Fragment: UNP residues 1-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae FostersO (yeast)
Strain: FostersO / Gene: FOSTERSO_2154 / Production host: Escherichia coli (E. coli) / References: UniProt: E7NIN2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20%(w/v) PEG-3500, 8%(v/v) Tacsimate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 28156 / % possible obs: 99.9 % / Redundancy: 21.5 % / Net I/σ(I): 82.913

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.761→37.597 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.31
Details: AUTHORS TREATED THE DATA SET AS AN ANOMALOUS ONE IN REFINEMENT, HOWEVER, IT WAS TREATED AS A NATIVE ONE IN DATA COLLECTION STATISTICS.
RfactorNum. reflection% reflection
Rfree0.2137 2749 10.06 %
Rwork0.1822 --
obs0.1853 27333 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.761→37.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1057 0 1 80 1138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071081
X-RAY DIFFRACTIONf_angle_d1.0221453
X-RAY DIFFRACTIONf_dihedral_angle_d13.247419
X-RAY DIFFRACTIONf_chiral_restr0.044157
X-RAY DIFFRACTIONf_plane_restr0.004186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7607-1.79110.27111340.24371201X-RAY DIFFRACTION99
1.7911-1.82370.21411460.20971251X-RAY DIFFRACTION100
1.8237-1.85880.25611360.19331220X-RAY DIFFRACTION100
1.8588-1.89670.1981440.18481212X-RAY DIFFRACTION100
1.8967-1.93790.23581480.18731240X-RAY DIFFRACTION100
1.9379-1.9830.19541400.19251252X-RAY DIFFRACTION100
1.983-2.03260.24241280.18711238X-RAY DIFFRACTION100
2.0326-2.08760.19951340.19091207X-RAY DIFFRACTION100
2.0876-2.1490.23481320.19531248X-RAY DIFFRACTION100
2.149-2.21830.24421320.18561236X-RAY DIFFRACTION100
2.2183-2.29760.24991320.19271237X-RAY DIFFRACTION100
2.2976-2.38960.24231260.19291220X-RAY DIFFRACTION100
2.3896-2.49830.21451400.21253X-RAY DIFFRACTION100
2.4983-2.630.22211420.18871199X-RAY DIFFRACTION100
2.63-2.79470.26191380.19271264X-RAY DIFFRACTION100
2.7947-3.01040.24231380.19531225X-RAY DIFFRACTION100
3.0104-3.31320.20931440.19151221X-RAY DIFFRACTION100
3.3132-3.79230.1931280.16191237X-RAY DIFFRACTION100
3.7923-4.77630.16881420.14231227X-RAY DIFFRACTION100
4.7763-37.60610.20361450.19061196X-RAY DIFFRACTION98

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