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- PDB-8k7z: De novo design protein -N1 -

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Basic information

Entry
Database: PDB / ID: 8k7z
TitleDe novo design protein -N1
ComponentsDe novo design protein
KeywordsDE NOVO PROTEIN / De novo design protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 31, 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)17,4131
Polymers17,4131
Non-polymers00
Water4,900272
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.436, 60.518, 37.996
Angle α, β, γ (deg.)90.000, 106.030, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-450-

HOH

21A-467-

HOH

31A-469-

HOH

41A-472-

HOH

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Components

#1: Protein De novo design protein


Mass: 17413.021 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.: 272 / 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: 2.17 Å3/Da / Density % sol: 43.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 0.1M Sodium citrate pH5.6 20%w/v PEG 4000

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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: 1.3→32.89 Å / Num. obs: 36124 / % possible obs: 98.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 13.63 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.2
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 1473 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→23.3 Å / SU ML: 0.1233 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.4866
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2007 1774 4.91 %
Rwork0.1756 34346 -
obs0.1768 36120 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.79 Å2
Refinement stepCycle: LAST / Resolution: 1.3→23.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1153 0 0 272 1425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461165
X-RAY DIFFRACTIONf_angle_d0.74721607
X-RAY DIFFRACTIONf_chiral_restr0.0604221
X-RAY DIFFRACTIONf_plane_restr0.0064208
X-RAY DIFFRACTIONf_dihedral_angle_d3.9524179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.340.27221020.22612259X-RAY DIFFRACTION84.35
1.34-1.370.24841470.21972597X-RAY DIFFRACTION97.44
1.37-1.420.23761300.19842667X-RAY DIFFRACTION99.96
1.42-1.470.19711350.18292675X-RAY DIFFRACTION100
1.47-1.530.21480.18252665X-RAY DIFFRACTION100
1.53-1.60.21391500.17492650X-RAY DIFFRACTION100
1.6-1.680.18341350.17622668X-RAY DIFFRACTION100
1.68-1.790.18771200.18142697X-RAY DIFFRACTION99.96
1.79-1.930.18241490.17912675X-RAY DIFFRACTION100
1.93-2.120.19491490.17032669X-RAY DIFFRACTION100
2.12-2.430.19691250.16912698X-RAY DIFFRACTION100
2.43-3.050.21191370.17852696X-RAY DIFFRACTION99.93
3.06-23.30.19581470.16622730X-RAY DIFFRACTION99.9

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