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- PDB-8fvt: Multi-state design of two-state switchable hinge proteins -

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Basic information

Entry
Database: PDB / ID: 8fvt
TitleMulti-state design of two-state switchable hinge proteins
Components3hb12
KeywordsDE NOVO PROTEIN / Metamorphic proteins / switchable hinge proteins / protein dynamics / three-helix bundles
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsBera, A.K. / Broerman, A. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2023
Title: Design of stimulus-responsive two-state hinge proteins.
Authors: Praetorius, F. / Leung, P.J.Y. / Tessmer, M.H. / Broerman, A. / Demakis, C. / Dishman, A.F. / Pillai, A. / Idris, A. / Juergens, D. / Dauparas, J. / Li, X. / Levine, P.M. / Lamb, M. / ...Authors: Praetorius, F. / Leung, P.J.Y. / Tessmer, M.H. / Broerman, A. / Demakis, C. / Dishman, A.F. / Pillai, A. / Idris, A. / Juergens, D. / Dauparas, J. / Li, X. / Levine, P.M. / Lamb, M. / Ballard, R.K. / Gerben, S.R. / Nguyen, H. / Kang, A. / Sankaran, B. / Bera, A.K. / Volkman, B.F. / Nivala, J. / Stoll, S. / Baker, D.
History
DepositionJan 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Refinement description / Category: pdbx_initial_refinement_model / Item: _pdbx_initial_refinement_model.type
Revision 1.2Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3hb12
B: 3hb12


Theoretical massNumber of molelcules
Total (without water)22,3872
Polymers22,3872
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.678, 67.678, 82.374
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein 3hb12


Mass: 11193.331 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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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: 2.19 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8 M Ammonium citrate tribasic pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 3.07→47.86 Å / Num. obs: 3505 / % possible obs: 99.6 % / Redundancy: 8.8 % / Biso Wilson estimate: 95.25 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.145 / Net I/σ(I): 17.39
Reflection shellResolution: 3.07→3.28 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 5.59 / Num. unique obs: 1727 / CC1/2: 0.987 / Rpim(I) all: 0.145 / % possible all: 99.48

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Processing

Software
NameVersionClassification
PHENIXdev_4761refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.07→47.86 Å / SU ML: 0.304 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.7284
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2737 341 9.73 %
Rwork0.2244 3164 -
obs0.2291 3505 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.94 Å2
Refinement stepCycle: LAST / Resolution: 3.07→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 0 0 1518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00371518
X-RAY DIFFRACTIONf_angle_d0.57642026
X-RAY DIFFRACTIONf_chiral_restr0.0266226
X-RAY DIFFRACTIONf_plane_restr0.0064282
X-RAY DIFFRACTIONf_dihedral_angle_d3.9332222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.07-3.860.31661850.29881543X-RAY DIFFRACTION99.54
3.87-47.860.25641560.19941621X-RAY DIFFRACTION99.78

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