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- PDB-5xbv: Crystal structure of Wss1 mutant from saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 5xbv
TitleCrystal structure of Wss1 mutant from saccharomyces cerevisiae
ComponentsWss1p
KeywordsHYDROLASE / protease
Function / homology:
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.804 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 mutant from saccharomyces cerevisiae
Authors: Dong, Y.H. / Yang, X.Y. / Wang, W.J.
History
DepositionMar 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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

Downloads & links

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Assembly

Deposited unit
A: Wss1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5102
Polymers17,4441
Non-polymers651
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-34 kcal/mol
Surface area7850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.202, 86.202, 36.287
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: 17444.383 Da / Num. of mol.: 1 / Fragment: UNP residues 2-149 / Mutation: E116Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's 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.: 141 / 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: 2.03 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10%(w/v) PEG-8000, 20mM Tris-HCl, pH 7.0, and 0.2M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 14399 / % possible obs: 100 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.021 / Net I/σ(I): 35.98
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 702 / CC1/2: 0.922 / Rpim(I) all: 0.171 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.804→24.884 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2003 688 4.79 %
Rwork0.1732 --
obs0.1744 14372 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.804→24.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 0 1 141 1190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071080
X-RAY DIFFRACTIONf_angle_d0.8331454
X-RAY DIFFRACTIONf_dihedral_angle_d2.189941
X-RAY DIFFRACTIONf_chiral_restr0.056156
X-RAY DIFFRACTIONf_plane_restr0.004186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8041-1.94330.23081460.19972691X-RAY DIFFRACTION100
1.9433-2.13880.20471210.18492734X-RAY DIFFRACTION100
2.1388-2.44810.22941350.17962734X-RAY DIFFRACTION100
2.4481-3.08340.18631690.18562709X-RAY DIFFRACTION100
3.0834-24.88670.19431170.15962816X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -28.9539 Å / Origin y: 3.4725 Å / Origin z: 2.9354 Å
111213212223313233
T0.0977 Å2-0.0175 Å2-0.0142 Å2-0.1439 Å20.0042 Å2--0.1232 Å2
L0.6129 °2-0.0864 °20.3252 °2-1.0365 °2-0.1408 °2--0.5657 °2
S0.0474 Å °0.0625 Å °-0.0407 Å °-0.0432 Å °-0.0041 Å °0.1988 Å °-0.0369 Å °0.0242 Å °0.0484 Å °
Refinement TLS groupSelection details: all

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