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

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Basic information

Entry
Database: PDB / ID: 8fiq
TitleMulti-state design of two-state switchable hinge proteins
Componentscs207AB
KeywordsDE NOVO PROTEIN / Metamorphic proteins / switchable hinge proteins / protein dynamics
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 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: cs207AB
B: cs207AB


Theoretical massNumber of molelcules
Total (without water)46,4152
Polymers46,4152
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-27 kcal/mol
Surface area10140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.882, 71.882, 127.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein cs207AB


Mass: 23207.520 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: 1.78 Å3/Da / Density % sol: 30.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Magnesium sulfate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 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: 2.66→47.72 Å / Num. obs: 9942 / % possible obs: 97.86 % / Redundancy: 13.9 % / Biso Wilson estimate: 88.06 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1361 / Rpim(I) all: 0.0378 / Net I/σ(I): 11.84
Reflection shellResolution: 2.66→2.8 Å / Rmerge(I) obs: 4.34 / Num. unique obs: 1246 / CC1/2: 0.661 / Rpim(I) all: 1.22 / % possible all: 89.38

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→47.72 Å / SU ML: 0.4523 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 42.1398
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3061 995 10.01 %
Rwork0.2683 8947 -
obs0.272 9942 97.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 108.65 Å2
Refinement stepCycle: LAST / Resolution: 2.66→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1538 0 0 0 1538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00161540
X-RAY DIFFRACTIONf_angle_d0.36082060
X-RAY DIFFRACTIONf_chiral_restr0.0291246
X-RAY DIFFRACTIONf_plane_restr0.0024272
X-RAY DIFFRACTIONf_dihedral_angle_d14.9514615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.80.44271260.46361123X-RAY DIFFRACTION89.6
2.8-2.980.51931420.40551264X-RAY DIFFRACTION98.6
2.98-3.210.3981400.34461267X-RAY DIFFRACTION99.08
3.21-3.530.33971410.28561274X-RAY DIFFRACTION99.3
3.53-4.040.32151410.28051287X-RAY DIFFRACTION99.1
4.04-5.090.2971480.25191326X-RAY DIFFRACTION99.59
5.09-47.720.25761570.23321406X-RAY DIFFRACTION99.62

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