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- PDB-8gac: Crystal structure of a high affinity CTLA-4 binder -

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Basic information

Entry
Database: PDB / ID: 8gac
TitleCrystal structure of a high affinity CTLA-4 binder
ComponentsCTLA-4 binder
KeywordsPROTEIN BINDING / De novo protein design / high affinity binder / CTLA-4
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsYang, W. / Almo, S.C. / Ghosh, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10 OD020068 United States
CitationJournal: To Be Published
Title: Crystal structure of a high affinity CTLA-4 binder
Authors: Yang, W. / Almo, S.C. / Ghosh, A. / Baker, D.
History
DepositionFeb 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CTLA-4 binder
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6992
Polymers12,6361
Non-polymers621
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Superdex S200
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.865, 52.037, 53.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CTLA-4 binder


Mass: 12636.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.01 % / Description: Thin plates
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30 % (w/v) PEG 3350, 0.22 M MgCl2 and 0.0.8 M Bis-Tris pH 5.5 and 0.15 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2022 / Details: KB MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→19.85 Å / Num. obs: 9931 / % possible obs: 99.6 % / Redundancy: 10.6 % / Biso Wilson estimate: 26.37 Å2 / CC1/2: 0.99 / CC star: 1 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.4
Reflection shellResolution: 1.85→1.92 Å / Num. unique obs: 1170 / CC1/2: 0.43 / CC star: 0.78

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
autoPROCdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→19.85 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2186 430 5.03 %
Rwork0.1914 --
obs-9929 99.9 %
Refinement stepCycle: LAST / Resolution: 1.85→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms868 0 0 63 931

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