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- PDB-7n1k: Crystal structure of a de novo-designed mini-protein targeting FGFR -

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Basic information

Entry
Database: PDB / ID: 7n1k
TitleCrystal structure of a de novo-designed mini-protein targeting FGFR
ComponentsBinder
KeywordsDE NOVO PROTEIN / Binder
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsPark, J.S. / Lee, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2022
Title: Design of protein-binding proteins from the target structure alone.
Authors: Cao, L. / Coventry, B. / Goreshnik, I. / Huang, B. / Sheffler, W. / Park, J.S. / Jude, K.M. / Markovic, I. / Kadam, R.U. / Verschueren, K.H.G. / Verstraete, K. / Walsh, S.T.R. / Bennett, N. ...Authors: Cao, L. / Coventry, B. / Goreshnik, I. / Huang, B. / Sheffler, W. / Park, J.S. / Jude, K.M. / Markovic, I. / Kadam, R.U. / Verschueren, K.H.G. / Verstraete, K. / Walsh, S.T.R. / Bennett, N. / Phal, A. / Yang, A. / Kozodoy, L. / DeWitt, M. / Picton, L. / Miller, L. / Strauch, E.M. / DeBouver, N.D. / Pires, A. / Bera, A.K. / Halabiya, S. / Hammerson, B. / Yang, W. / Bernard, S. / Stewart, L. / Wilson, I.A. / Ruohola-Baker, H. / Schlessinger, J. / Lee, S. / Savvides, S.N. / Garcia, K.C. / Baker, D.
History
DepositionMay 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author / Item: _citation.title
Revision 1.2May 25, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Binder


Theoretical massNumber of molelcules
Total (without water)7,5361
Polymers7,5361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.482, 42.482, 83.143
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4

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Components

#1: Protein Binder


Mass: 7535.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
Details: 1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-Propanediol, Tris-BICINE (pH 8.5), MPD, PEG 1000, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.01→50 Å / Num. obs: 1644 / % possible obs: 93.8 % / Redundancy: 5.5 % / CC1/2: 0.999 / Net I/σ(I): 17.85
Reflection shellResolution: 3.01→3.19 Å / Num. unique obs: 247 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREDICTED MODEL

Resolution: 3.01→42.48 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 24.1369
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2983 81 5 %
Rwork0.2714 1538 -
obs0.2724 1619 93.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.05 Å2
Refinement stepCycle: LAST / Resolution: 3.01→42.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms381 0 0 0 381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025385
X-RAY DIFFRACTIONf_angle_d0.3688530
X-RAY DIFFRACTIONf_chiral_restr0.032373
X-RAY DIFFRACTIONf_plane_restr0.005366
X-RAY DIFFRACTIONf_dihedral_angle_d2.905662
LS refinement shellResolution: 3.01→42.48 Å
RfactorNum. reflection% reflection
Rfree0.2983 81 -
Rwork0.2714 1538 -
obs--93.42 %

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