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- PDB-2wvn: Structure of the HET-s N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2wvn
TitleStructure of the HET-s N-terminal domain
ComponentsSMALL S PROTEIN
KeywordsPRION-BINDING PROTEIN / PRION REGULATORY DOMAIN / HETEROKARYON INCOMPATIBILITY
Function / homology
Function and homology information


identical protein binding / cytoplasm
Similarity search - Function
Prion-inhibition and propagation, HeLo domain / Het-s prion-forming domain / Prion-inhibition and propagation, HeLo domain / HeLo domain superfamily / Het-s 218-289 / Prion-inhibition and propagation / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Heterokaryon incompatibility protein s
Similarity search - Component
Biological speciesPODOSPORA ANSERINA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.62 Å
AuthorsGreenwald, J. / Buhtz, C. / Ritter, C. / Kwiatkowski, W. / Choe, S. / Saupe, S.J. / Riek, R.
CitationJournal: Mol.Cell / Year: 2010
Title: The Mechanism of Prion Inhibition by Het-S.
Authors: Greenwald, J. / Buhtz, C. / Ritter, C. / Kwiatkowski, W. / Choe, S. / Maddelein, M.L. / Ness, F. / Cescau, S. / Soragni, A. / Leitz, D. / Saupe, S.J. / Riek, R.
History
DepositionOct 19, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SMALL S PROTEIN


Theoretical massNumber of molelcules
Total (without water)25,5331
Polymers25,5331
Non-polymers00
Water00
1
A: SMALL S PROTEIN

A: SMALL S PROTEIN


Theoretical massNumber of molelcules
Total (without water)51,0662
Polymers51,0662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_555-x,z,y1
Buried area1730 Å2
ΔGint-1.9 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.660, 122.660, 122.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432

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Components

#1: Protein SMALL S PROTEIN / HET-S


Mass: 25533.041 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PODOSPORA ANSERINA (fungus) / Plasmid: PRSET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: Q03689

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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: 3.24 Å3/Da / Density % sol: 61.72 % / Description: NONE
Crystal growTemperature: 292 K / pH: 8
Details: CRYSTALLIZED AT 292K WITH 20 MM TRIS PH 8.0, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.62→40 Å / Num. obs: 10044 / % possible obs: 99.7 % / Observed criterion σ(I): -10 / Redundancy: 10.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.1
Reflection shellResolution: 2.62→2.77 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 3.9 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.62→38.78 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.911 / SU B: 23.157 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.449 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 477 4.7 %RANDOM
Rwork0.216 ---
obs0.219 9566 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.77 Å2
Refinement stepCycle: LAST / Resolution: 2.62→38.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1683 0 0 0 1683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221720
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.9692318
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0165215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44224.40584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.87915323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9311515
X-RAY DIFFRACTIONr_chiral_restr0.140.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021289
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2420.2722
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21180
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.217
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3280.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8771.51105
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63421716
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2473690
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7414.5602
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.62→2.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 30 -
Rwork0.333 687 -
obs--97.95 %

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