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- PDB-7s5b: Unbound State of a De novo designed Protein Binder to the Human I... -

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Basic information

Entry
Database: PDB / ID: 7s5b
TitleUnbound State of a De novo designed Protein Binder to the Human Interleukin-7 Receptor
ComponentsMiniprotein Binder
KeywordsDE NOVO PROTEIN / minibinder protein inhibitor cytokine receptor interleukin-7
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWalsh, S.T.R. / Cao, L. / Baker, D.
Funding support United States, 6items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)FA8750-17-C-0219 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
Howard Hughes Medical Institute (HHMI)DB United States
National Institutes of Health/National Cancer Institute (NIH/NCI)ACB-12002 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AGM-12006, P30GM138396 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10 OD012289 United States
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
DepositionSep 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 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

Downloads & links

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Assembly

Deposited unit
A: Miniprotein Binder
B: Miniprotein Binder


Theoretical massNumber of molelcules
Total (without water)12,8872
Polymers12,8872
Non-polymers00
Water1,35175
1
A: Miniprotein Binder


Theoretical massNumber of molelcules
Total (without water)6,4431
Polymers6,4431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Miniprotein Binder


Theoretical massNumber of molelcules
Total (without water)6,4431
Polymers6,4431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.226, 92.226, 108.436
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11B-142-

HOH

21B-143-

HOH

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Components

#1: Protein Miniprotein Binder


Mass: 6443.422 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 / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.44 Å3/Da / Density % sol: 64.2 % / Description: prism
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 3.0 M sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03331 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 26, 2020 / Details: KB
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03331 Å / Relative weight: 1
ReflectionResolution: 1.5→36.15 Å / Num. obs: 28231 / % possible obs: 98.95 % / Redundancy: 6.7 % / Biso Wilson estimate: 27.7 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04556 / Rpim(I) all: 0.01904 / Rrim(I) all: 0.04949 / Net I/σ(I): 16.19
Reflection shellResolution: 1.501→1.554 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.61 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 2735 / CC1/2: 0.45 / CC star: 0.788 / Rpim(I) all: 0.671 / % possible all: 97.35

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Processing

Software
NameVersionClassification
PHENIX1.18rc5_3822refinement
XDS20200131data reduction
XDS20200131data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model

Resolution: 1.5→36.15 Å / SU ML: 0.2228 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0239
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1983 1412 5 %
Rwork0.1769 26802 -
obs0.178 28214 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.92 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms886 0 0 75 961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132890
X-RAY DIFFRACTIONf_angle_d1.38851185
X-RAY DIFFRACTIONf_chiral_restr0.0547136
X-RAY DIFFRACTIONf_plane_restr0.0076149
X-RAY DIFFRACTIONf_dihedral_angle_d4.1699118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.550.42541370.39162587X-RAY DIFFRACTION97.53
1.55-1.620.26981400.26862658X-RAY DIFFRACTION98.45
1.62-1.690.24981390.23152646X-RAY DIFFRACTION98.72
1.69-1.780.25681400.21572651X-RAY DIFFRACTION98.76
1.78-1.890.24151400.1962663X-RAY DIFFRACTION99.26
1.89-2.040.18661410.17432678X-RAY DIFFRACTION99.19
2.04-2.240.20221410.16792689X-RAY DIFFRACTION99.3
2.24-2.570.19611430.15992709X-RAY DIFFRACTION99.55
2.57-3.230.20821440.18592728X-RAY DIFFRACTION99.72
3.23-36.150.17391470.16172793X-RAY DIFFRACTION99.09

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