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- PDB-8k8f: De novo design protein -N7 -

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Basic information

Entry
Database: PDB / ID: 8k8f
TitleDe novo design protein -N7
ComponentsDe novo design protein N7
KeywordsDE NOVO PROTEIN / De novo design protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 1.0Jul 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo design protein N7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9072
Polymers20,8151
Non-polymers921
Water2,468137
1
A: De novo design protein N7
hetero molecules

A: De novo design protein N7
hetero molecules

A: De novo design protein N7
hetero molecules

A: De novo design protein N7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6288
Polymers83,2604
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area7900 Å2
ΔGint-64 kcal/mol
Surface area26920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.427, 72.427, 33.677
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
Space group name HallP4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-434-

HOH

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Components

#1: Protein De novo design protein N7


Mass: 20814.979 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.12 Å3/Da / Density % sol: 42.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 1.6M Ammonium sulfate ,0.1M MES monohydrate PH6.5, 10% v/v 1,4Dioxane

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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: 1.315→72.452 Å / Num. obs: 41632 / % possible obs: 99.3 % / Redundancy: 12.4 % / Biso Wilson estimate: 15.61 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.2
Reflection shellResolution: 1.315→1.338 Å / Num. unique obs: 376 / CC1/2: 0.388

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→28.14 Å / SU ML: 0.145 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.9765
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2301 1542 4.94 %
Rwork0.201 29663 -
obs0.2024 31205 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.39 Å2
Refinement stepCycle: LAST / Resolution: 1.45→28.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1300 0 6 137 1443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411322
X-RAY DIFFRACTIONf_angle_d0.78131801
X-RAY DIFFRACTIONf_chiral_restr0.0633224
X-RAY DIFFRACTIONf_plane_restr0.0072234
X-RAY DIFFRACTIONf_dihedral_angle_d4.7425197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.50.38181240.34312660X-RAY DIFFRACTION99.68
1.5-1.550.31251520.3052682X-RAY DIFFRACTION99.65
1.55-1.610.29181310.25262684X-RAY DIFFRACTION99.86
1.61-1.690.23061370.2282693X-RAY DIFFRACTION99.79
1.69-1.770.23871550.21712687X-RAY DIFFRACTION99.86
1.77-1.890.20261420.19642662X-RAY DIFFRACTION99.89
1.89-2.030.22551370.20452659X-RAY DIFFRACTION98.69
2.03-2.240.24361350.19022695X-RAY DIFFRACTION99.23
2.24-2.560.2361460.19182694X-RAY DIFFRACTION99.58
2.56-3.220.23771260.19362733X-RAY DIFFRACTION99.93
3.22-28.140.20011570.17972814X-RAY DIFFRACTION99.87
Refinement TLS params.Method: refined / Origin x: 17.8261109373 Å / Origin y: 17.2180366205 Å / Origin z: 0.438293682654 Å
111213212223313233
T0.101731191735 Å2-0.00142870766621 Å20.00162525974952 Å2-0.101339389736 Å2-0.0105985081507 Å2--0.0787823662137 Å2
L0.813294122751 °2-0.0072102068326 °20.0639281198182 °2-0.718358063358 °2-0.250803624389 °2--0.205421574278 °2
S-0.00419432244037 Å °-0.0092308822404 Å °-0.101613061885 Å °0.00686193751825 Å °-0.0112479169058 Å °0.000155489482258 Å °-0.0192536583549 Å °-0.00166895923684 Å °2.63123069581E-9 Å °
Refinement TLS groupSelection details: all

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