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

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Basic information

Entry
Database: PDB / ID: 8fin
TitleMulti-state design of two-state switchable hinge proteins
Componentscs207A
KeywordsDE NOVO PROTEIN / Metamorphic proteins / switchable hinge proteins / protein dynamics
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBera, A.K. / Leung, P.J.Y. / 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
DepositionDec 16, 2022Deposition 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: cs207A
B: cs207A


Theoretical massNumber of molelcules
Total (without water)42,0802
Polymers42,0802
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)22.860, 81.735, 154.948
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein cs207A


Mass: 21039.877 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)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 1.72 Å3/Da / Density % sol: 28.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M SPG buffer pH 7, 25% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→43.66 Å / Num. obs: 13723 / % possible obs: 99.85 % / Redundancy: 13.7 % / Biso Wilson estimate: 40.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.032 / Net I/σ(I): 15.19
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 4.77 / Num. unique obs: 1431 / CC1/2: 0.99 / Rpim(I) all: 0.157 / % possible all: 99.93

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→43.66 Å / SU ML: 0.2751 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9111
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.275 1203 8.77 %
Rwork0.2389 12520 -
obs0.2421 13723 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2659 0 0 24 2683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00132661
X-RAY DIFFRACTIONf_angle_d0.29013570
X-RAY DIFFRACTIONf_chiral_restr0.0297435
X-RAY DIFFRACTIONf_plane_restr0.0021472
X-RAY DIFFRACTIONf_dihedral_angle_d13.89051052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.390.30351260.23521305X-RAY DIFFRACTION99.93
2.39-2.50.33611340.25011399X-RAY DIFFRACTION100
2.5-2.630.29231280.24921337X-RAY DIFFRACTION100
2.63-2.80.34551320.26181378X-RAY DIFFRACTION99.93
2.8-3.010.29561310.27981364X-RAY DIFFRACTION99.87
3.01-3.320.3061350.25341402X-RAY DIFFRACTION99.74
3.32-3.80.25961340.24221399X-RAY DIFFRACTION99.87
3.8-4.780.27011350.21161412X-RAY DIFFRACTION99.87
4.79-43.660.23291480.23171524X-RAY DIFFRACTION99.52

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