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- PDB-2wvq: Structure of the HET-s N-terminal domain. Mutant D23A, P33H -

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Basic information

Entry
Database: PDB / ID: 2wvq
TitleStructure of the HET-s N-terminal domain. Mutant D23A, P33H
ComponentsSMALL S PROTEIN
KeywordsPRION-BINDING PROTEIN / PRION / PRION REGULATORY DOMAIN / HETEROKARYON INCOMPATIBILITY / PRION- BINDING PROTEIN
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Heterokaryon incompatibility protein s
Similarity search - Component
Biological speciesPODOSPORA ANSERINA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 27, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SMALL S PROTEIN
B: SMALL S PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2224
Polymers50,9142
Non-polymers3092
Water3,567198
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-11.3 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.330, 83.150, 67.360
Angle α, β, γ (deg.)90.00, 104.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.3518, -0.8016, -0.4833), (-0.7859, -0.02748, 0.6177), (-0.5085, 0.5972, -0.6204)
Vector: 15.02, -30.54, 67.76)

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Components

#1: Protein SMALL S PROTEIN / HET-S MUTANT D23A / P33H


Mass: 25456.965 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 13-221 / Mutation: YES
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) / Variant (production host): pLysS / References: UniProt: Q03689
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Dithioerythritol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 23 TO ALA ENGINEERED RESIDUE IN CHAIN A, PRO 33 TO HIS ...ENGINEERED RESIDUE IN CHAIN A, ASP 23 TO ALA ENGINEERED RESIDUE IN CHAIN A, PRO 33 TO HIS ENGINEERED RESIDUE IN CHAIN B, ASP 23 TO ALA ENGINEERED RESIDUE IN CHAIN B, PRO 33 TO HIS

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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: 2.67 Å3/Da / Density % sol: 53.57 % / Description: NONE
Crystal growTemperature: 276 K / Details: CRYSTALLIZED AT 276K IN 25% ETHYLENE GLYCOL

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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→65 Å / Num. obs: 34078 / % possible obs: 95.2 % / Observed criterion σ(I): -10 / Redundancy: 3.2 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.5
Reflection shellResolution: 2→2.12 Å / Redundancy: 3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.7 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WVN

2wvn


Resolution: 2→65.23 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU B: 12.51 / SU ML: 0.182 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. EXTRA ELECTRON DENSITY MODELED AS TWO DITHIOTHREITO MOLECULES. IDENTITY NOT CONFIRMED.
RfactorNum. reflection% reflectionSelection details
Rfree0.26947 1697 4.9 %RANDOM
Rwork0.225 ---
obs0.22725 32594 96.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.008 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å2-0.46 Å2
2---0.14 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2→65.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3300 0 16 198 3514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223433
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.9654626
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8325431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49324.31174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.31715639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5461531
X-RAY DIFFRACTIONr_chiral_restr0.1570.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022590
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.21589
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.22308
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2191
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3110.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8211.52203
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38523387
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.20131393
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3654.51235
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 145 -
Rwork0.312 2498 -
obs--99.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.99870.42050.85111.2738-0.40241.94050.05090.00710.0307-0.01010.02250.0634-0.0413-0.0997-0.0733-0.14950.0354-0.0119-0.06420.0131-0.1173-5.2080.85929.978
21.89070.81510.67083.4145-0.23761.41490.022-0.10170.05630.3882-0.0460.0155-0.15040.00660.0241-0.0956-0.0036-0.0258-0.0296-0.0094-0.14441.664-7.252.614
33.8333-0.40960.80111.37150.01862.84570.0050.54880.1796-0.2379-0.0134-0.1834-0.24240.42620.0085-0.1367-0.01210.0328-0.03540.0757-0.07745.7997.98420.897
45.84373.08283.73694.24731.47315.44630.1739-0.6509-0.24650.4463-0.14410.0350.2148-0.3073-0.0297-0.12620.00360.0303-0.04090.0445-0.1976-3.099-21.58857.396
527.17427.19274.64296.49660.47422.19920.2996-0.2646-1.1334-0.0275-0.0866-0.4120.22040.0992-0.2129-0.1340.0465-0.0186-0.1186-0.0032-0.1239-2.768-7.60129.621
620.794816.11369.102915.32198.53668.306-0.43640.3745-0.4286-0.61220.4314-0.426-0.41980.22440.0051-0.13270.0202-0.025-0.09450.015-0.1757.652-9.21646.535
715.91310.7529-2.18752.8894-1.16786.2037-0.0631.6903-1.1198-0.65910.02210.0270.5881-0.22150.0409-0.07610.01690.02090.1245-0.2437-0.1505-3.552-6.58710.854
82.9651-2.88920.560917.3862-4.07445.0189-0.0951-0.1520.33280.6079-0.3047-1.30060.04210.71110.3998-0.14820.0459-0.10870.08380.0334-0.091316.559-19.79558.792
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 103
2X-RAY DIFFRACTION2B14 - 103
3X-RAY DIFFRACTION3A104 - 138
4X-RAY DIFFRACTION4B104 - 138
5X-RAY DIFFRACTION5A152 - 174
6X-RAY DIFFRACTION6B152 - 174
7X-RAY DIFFRACTION7A176 - 220
8X-RAY DIFFRACTION8B176 - 220

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