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

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Basic information

Entry
Database: PDB / ID: 8fih
TitleMulti-state design of two-state switchable hinge proteins
Components3hb05
KeywordsDE NOVO PROTEIN / Metamorphic proteins / switchable hinge proteins / protein dynamics
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
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: 3hb05
B: 3hb05
C: 3hb05
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6415
Polymers35,4513
Non-polymers1902
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.018, 119.757, 38.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein 3hb05


Mass: 11817.161 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M Lithium sulfate, 0.1 M Sodium Phosphate-citrate pH 4.2, 20% PEG 1000

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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 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: 2.2→44.35 Å / Num. obs: 15520 / % possible obs: 95.27 % / Redundancy: 1.4 % / Biso Wilson estimate: 26.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03 / Net I/σ(I): 9.89
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 1 % / Rmerge(I) obs: 1.161 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 1653 / CC1/2: 0.852

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→44.35 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.5848
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2484 1006 6.48 %
Rwork0.1907 14514 -
obs0.1946 15520 95.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.26 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 10 81 2573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00452508
X-RAY DIFFRACTIONf_angle_d0.55923339
X-RAY DIFFRACTIONf_chiral_restr0.0267351
X-RAY DIFFRACTIONf_plane_restr0.0052457
X-RAY DIFFRACTIONf_dihedral_angle_d14.24791020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.320.25131030.191550X-RAY DIFFRACTION72.82
2.32-2.460.28191320.20012037X-RAY DIFFRACTION94.76
2.46-2.650.31711450.19832121X-RAY DIFFRACTION99.56
2.65-2.920.25581630.20082141X-RAY DIFFRACTION99.91
2.92-3.340.26051480.19452168X-RAY DIFFRACTION99.91
3.34-4.210.2141510.15882193X-RAY DIFFRACTION99.87
4.21-44.350.24021640.20772304X-RAY DIFFRACTION99.4
Refinement TLS params.Method: refined / Origin x: -6.04793159975 Å / Origin y: 30.8069095898 Å / Origin z: -27.229819874 Å
111213212223313233
T0.12087223227 Å20.00639314869133 Å20.0101517488962 Å2-0.112249062138 Å20.0168639790865 Å2--0.124898730833 Å2
L0.204905524233 °20.0807863229351 °2-0.176818382617 °2-0.13821032259 °20.108028742531 °2--0.149949651995 °2
S-0.00639088287511 Å °0.028565642256 Å °-0.0617872194708 Å °-0.0471857744342 Å °-0.00934808357039 Å °0.0112442582542 Å °0.00257568739116 Å °-0.0124287298427 Å °6.16714362767E-5 Å °
Refinement TLS groupSelection details: all

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