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- PDB-8k84: De novo design protein -N3 -

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Basic information

Entry
Database: PDB / ID: 8k84
TitleDe novo design protein -N3
ComponentsDe novo design protein
KeywordsDE NOVO PROTEIN / De novo design protein
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 28, 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
B: De novo design protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2773
Polymers38,1712
Non-polymers1061
Water4,630257
1
A: De novo design protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1922
Polymers19,0861
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: De novo design protein


Theoretical massNumber of molelcules
Total (without water)19,0861
Polymers19,0861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.899, 35.599, 70.422
Angle α, β, γ (deg.)90.000, 117.010, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein De novo design protein


Mass: 19085.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.05 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 0.2M Imidazole malate pH5.5 33% w/v PEG600

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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: 2→59.82 Å / Num. obs: 21086 / % possible obs: 99.3 % / Redundancy: 3 % / Biso Wilson estimate: 19.05 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.7
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 1527 / CC1/2: 0.584

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25.01 Å / SU ML: 0.2577 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7565
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2455 1175 5.58 %
Rwork0.1882 19891 -
obs0.1914 21066 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.91 Å2
Refinement stepCycle: LAST / Resolution: 2→25.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2614 0 7 257 2878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592655
X-RAY DIFFRACTIONf_angle_d0.73433607
X-RAY DIFFRACTIONf_chiral_restr0.0411431
X-RAY DIFFRACTIONf_plane_restr0.0059475
X-RAY DIFFRACTIONf_dihedral_angle_d4.0237375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.33271720.24882451X-RAY DIFFRACTION99.54
2.09-2.20.26561570.212453X-RAY DIFFRACTION99.5
2.2-2.340.22881450.18872445X-RAY DIFFRACTION99.23
2.34-2.520.26611490.18852482X-RAY DIFFRACTION99.13
2.52-2.770.24351420.18622487X-RAY DIFFRACTION99.43
2.77-3.170.25451010.18642534X-RAY DIFFRACTION99.17
3.17-3.990.22441560.16652502X-RAY DIFFRACTION98.99
4-25.010.22541530.18632537X-RAY DIFFRACTION97.32

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