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

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Basic information

Entry
Database: PDB / ID: 8fit
TitleMulti-state design of two-state switchable hinge proteins
Componentscs074A
KeywordsDE NOVO PROTEIN / Metamorphic proteins / switchable hinge proteins / protein dynamics
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsBera, A.K. / Praetorius, F. / 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: cs074A
B: cs074A
C: cs074A
D: cs074A


Theoretical massNumber of molelcules
Total (without water)117,4624
Polymers117,4624
Non-polymers00
Water724
1
A: cs074A
B: cs074A


Theoretical massNumber of molelcules
Total (without water)58,7312
Polymers58,7312
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-18 kcal/mol
Surface area12980 Å2
MethodPISA
2
C: cs074A
D: cs074A


Theoretical massNumber of molelcules
Total (without water)58,7312
Polymers58,7312
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-17 kcal/mol
Surface area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.117, 45.369, 61.803
Angle α, β, γ (deg.)109.269, 94.537, 104.093
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
cs074A


Mass: 29365.600 Da / Num. of mol.: 4
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.: 4 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Calcium acetate, 0.1 M Na cacodylate pH 6.5, 40% PEG 300

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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: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→57.45 Å / Num. obs: 20087 / % possible obs: 89.39 % / Redundancy: 2.2 % / Biso Wilson estimate: 76.39 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.064 / Net I/σ(I): 7.58
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 0.57 / Num. unique obs: 1563 / CC1/2: 0.769 / Rpim(I) all: 0.369 / % possible all: 90.08

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→57.45 Å / SU ML: 0.3975 / Cross valid method: FREE R-VALUE / σ(F): 0.19 / Phase error: 31.9954
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2958 1004 5 %
Rwork0.2451 19083 -
obs0.2475 20087 89.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.86 Å2
Refinement stepCycle: LAST / Resolution: 2.75→57.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3871 0 0 4 3875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00163879
X-RAY DIFFRACTIONf_angle_d0.41945190
X-RAY DIFFRACTIONf_chiral_restr0.0274623
X-RAY DIFFRACTIONf_plane_restr0.0028676
X-RAY DIFFRACTIONf_dihedral_angle_d13.21751567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.90.33691610.29042736X-RAY DIFFRACTION90.08
2.9-3.080.31281420.27722768X-RAY DIFFRACTION89.81
3.08-3.310.3761400.28172662X-RAY DIFFRACTION88.73
3.31-3.650.36621630.26562632X-RAY DIFFRACTION86.05
3.65-4.170.29911400.26562565X-RAY DIFFRACTION84.74
4.18-5.260.2591140.23212783X-RAY DIFFRACTION90.64
5.26-57.450.2531440.21642937X-RAY DIFFRACTION95.74

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