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- PDB-5ete: Structure of pathogen-related yeast protein, Pry1 in complex with... -

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Basic information

Entry
Database: PDB / ID: 5ete
TitleStructure of pathogen-related yeast protein, Pry1 in complex with a competitive inhibitor of cholesterol binding
ComponentsPry1p
KeywordsSterol binding protein / TAPs / testis specific proteins / Tpx / antigen 5 / Ag5 / pathogenesis related-1 / PR-1 / Sc7 / CAP / cysteine-rich secretory protein / CRISP
Function / homologyPathogenesis-related Protein p14a / CAP / 3-Layer(aba) Sandwich / Alpha Beta / 1,4-DIETHYLENE DIOXIDE / :
Function and homology information
Biological speciesSaccharomyces cerevisiae YJM1434 (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAsojo, O.A.
CitationJournal: Sci Rep / Year: 2016
Title: Structural and functional characterization of the CAP domain of pathogen-related yeast 1 (Pry1) protein.
Authors: Darwiche, R. / Kelleher, A. / Hudspeth, E.M. / Schneiter, R. / Asojo, O.A.
History
DepositionNov 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pry1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2565
Polymers15,9041
Non-polymers3524
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.740, 124.740, 59.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-302-

DIO

21A-302-

DIO

31A-518-

HOH

41A-538-

HOH

51A-544-

HOH

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Components

#1: Protein Pry1p


Mass: 15903.875 Da / Num. of mol.: 1 / Fragment: residues 158-306
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae YJM1434 (yeast)
Gene: PRY1, H819_YJM1434J00135 / Production host: Pichia (fungus) / References: UniProt: A0A0C6AG41
#2: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 4.17 Å3/Da / Density % sol: 70.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1.6M Ammonium sulphate, 0.1M MES pH 6.5, 10% v/v 1,4-dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54056 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.1→30.75 Å / Num. obs: 17583 / % possible obs: 99.8 % / Redundancy: 13.9 % / Net I/σ(I): 15.4

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Processing

Software
NameVersionClassification
PHENIX(dev_2405)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SMB

1smb


Resolution: 2.1→28.485 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1904 831 5.13 %RANDOM
Rwork0.1671 ---
obs0.1682 16203 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→28.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1079 0 24 167 1270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111137
X-RAY DIFFRACTIONf_angle_d0.9351548
X-RAY DIFFRACTIONf_dihedral_angle_d12.132647
X-RAY DIFFRACTIONf_chiral_restr0.052155
X-RAY DIFFRACTIONf_plane_restr0.006203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.23150.22181570.18792488X-RAY DIFFRACTION100
2.2315-2.40370.2081380.16612512X-RAY DIFFRACTION100
2.4037-2.64550.19971220.16892546X-RAY DIFFRACTION100
2.6455-3.02790.20621310.17042543X-RAY DIFFRACTION99
3.0279-3.81340.19541230.16792578X-RAY DIFFRACTION99
3.8134-28.48750.16691600.16012705X-RAY DIFFRACTION99

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