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- PDB-8k8g: De novo design protein -N9 -

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Basic information

Entry
Database: PDB / ID: 8k8g
TitleDe novo design protein -N9
ComponentsDe novo design protein
KeywordsDE NOVO PROTEIN / De novo design protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsWang, S. / Liu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Methods / Year: 2024
Title: De novo protein design with a denoising diffusion network independent of pretrained structure prediction models.
Authors: Liu, Y. / Wang, S. / Dong, J. / Chen, L. / Wang, X. / Wang, L. / Li, F. / Wang, C. / Zhang, J. / Wang, Y. / Wei, S. / Chen, Q. / Liu, H.
History
DepositionJul 29, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Assembly

Deposited unit
A: De novo design protein


Theoretical massNumber of molelcules
Total (without water)21,1461
Polymers21,1461
Non-polymers00
Water3,837213
1
A: De novo design protein

A: De novo design protein


Theoretical massNumber of molelcules
Total (without water)42,2922
Polymers42,2922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1830 Å2
ΔGint-12 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.011, 75.997, 129.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-311-

HOH

21A-372-

HOH

31A-385-

HOH

41A-417-

HOH

51A-425-

HOH

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Components

#1: Protein De novo design protein


Mass: 21146.010 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)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 20% w/v PEG 10000 0.1M Hepes ph7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.35→43.21 Å / Num. obs: 38537 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 15.47 Å2 / CC1/2: 1 / Net I/σ(I): 21.2
Reflection shellResolution: 1.35→1.37 Å / Num. unique obs: 1970 / CC1/2: 0.817

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→25.61 Å / SU ML: 0.1522 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8185
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2273 1939 5.04 %
Rwork0.2018 36538 -
obs0.2031 38477 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.31 Å2
Refinement stepCycle: LAST / Resolution: 1.35→25.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1432 0 0 213 1645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591461
X-RAY DIFFRACTIONf_angle_d0.84222010
X-RAY DIFFRACTIONf_chiral_restr0.0739255
X-RAY DIFFRACTIONf_plane_restr0.0096267
X-RAY DIFFRACTIONf_dihedral_angle_d11.1993502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.28671280.27532549X-RAY DIFFRACTION99.93
1.38-1.420.26231590.25032548X-RAY DIFFRACTION99.85
1.42-1.460.27831410.23332585X-RAY DIFFRACTION99.96
1.46-1.510.24511270.22862580X-RAY DIFFRACTION99.93
1.51-1.560.26671310.22182582X-RAY DIFFRACTION100
1.56-1.630.24881240.22082599X-RAY DIFFRACTION100
1.63-1.70.22081420.21152586X-RAY DIFFRACTION99.96
1.7-1.790.20111330.20362592X-RAY DIFFRACTION100
1.79-1.90.2191260.21422646X-RAY DIFFRACTION100
1.9-2.050.26421250.20942597X-RAY DIFFRACTION100
2.05-2.260.20151600.18722601X-RAY DIFFRACTION100
2.26-2.580.21611490.19662638X-RAY DIFFRACTION100
2.58-3.250.23051510.19672653X-RAY DIFFRACTION100
3.25-25.610.22111430.18862782X-RAY DIFFRACTION99.86

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