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- PDB-6v67: Apo Structure of the De Novo PD-1 Binding Miniprotein GR918.2 -

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Entry
Database: PDB / ID: 6v67
TitleApo Structure of the De Novo PD-1 Binding Miniprotein GR918.2
ComponentsPD-1 Binding Miniprotein GR918.2
KeywordsDE NOVO PROTEIN / PD-1 / Disulfide Miniprotein / Computational Design / Binder
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsBick, M.J. / Bryan, C.M. / Baker, D. / Dimaio, F. / Kang, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5U01GM094665 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM123089 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Computational design of a synthetic PD-1 agonist.
Authors: Bryan, C.M. / Rocklin, G.J. / Bick, M.J. / Ford, A. / Majri-Morrison, S. / Kroll, A.V. / Miller, C.J. / Carter, L. / Goreshnik, I. / Kang, A. / DiMaio, F. / Tarbell, K.V. / Baker, D.
History
DepositionDec 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author / database_2
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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 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:
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Assembly

Deposited unit
A: PD-1 Binding Miniprotein GR918.2
B: PD-1 Binding Miniprotein GR918.2


Theoretical massNumber of molelcules
Total (without water)9,8792
Polymers9,8792
Non-polymers00
Water1,58588
1
A: PD-1 Binding Miniprotein GR918.2


Theoretical massNumber of molelcules
Total (without water)4,9401
Polymers4,9401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PD-1 Binding Miniprotein GR918.2


Theoretical massNumber of molelcules
Total (without water)4,9401
Polymers4,9401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.849, 26.744, 51.537
Angle α, β, γ (deg.)90.000, 99.670, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-108-

HOH

21A-118-

HOH

31B-109-

HOH

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Components

#1: Protein/peptide PD-1 Binding Miniprotein GR918.2


Mass: 4939.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 1.8 Å3/Da / Density % sol: 29.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES/Imidazole pH 6.5, 0.03 M Diethylene Glycol, 0.03 M Triethylene Glycol, 0.03 M Tetraethylene Glycol, 0.03 M Pentaethylene Glycol, 10% PEG 20,000, 20% PEG MME 550

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryo-Jet crystal cryocoolers / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.02→50.81 Å / Num. obs: 33643 / % possible obs: 95 % / Redundancy: 4.1 % / Biso Wilson estimate: 10.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.031 / Rrim(I) all: 0.067 / Net I/σ(I): 10.7 / Num. measured all: 138087
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.02-1.031.40.593155610930.6520.5080.785160.8
5.47-50.814.50.04211692580.9960.0210.04828.299.3

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Processing

Software
NameVersionClassification
XDSMay 1, 2016data reduction
Aimless0.5.23data scaling
PHENIXdev_2849refinement
PDB_EXTRACT3.25data extraction
PHASER2.7.18phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Single helix, residues 18-31, of the computational model

Resolution: 1.07→50.805 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 16.08
RfactorNum. reflection% reflection
Rfree0.1498 1465 4.94 %
Rwork0.1455 --
obs0.1457 29628 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 39.88 Å2 / Biso mean: 16.0024 Å2 / Biso min: 8.08 Å2
Refinement stepCycle: final / Resolution: 1.07→50.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms658 0 0 88 746
Biso mean---25.77 -
Num. residues----85
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009769
X-RAY DIFFRACTIONf_angle_d1.0841058
X-RAY DIFFRACTIONf_chiral_restr0.099105
X-RAY DIFFRACTIONf_plane_restr0.006142
X-RAY DIFFRACTIONf_dihedral_angle_d15.344298
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.07-1.10820.25511260.1981272995
1.1082-1.15260.17071360.1495275796
1.1526-1.20510.16871480.1368276097
1.2051-1.26860.15741300.1285279498
1.2686-1.34810.14861540.1207286399
1.3481-1.45220.14181430.119282998
1.4522-1.59840.13961510.1204281898
1.5984-1.82970.13771660.1342284199
1.8297-2.30520.14911560.1444284298
2.3052-50.8050.14811550.1611293098

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