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- PDB-8k83: De novo design protein -N2 -

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Basic information

Entry
Database: PDB / ID: 8k83
TitleDe novo design protein -N2
ComponentsDe novo design protein
KeywordsDE NOVO PROTEIN / De novo design protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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)38,2745
Polymers37,7912
Non-polymers4833
Water4,378243
1
A: De novo design protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0912
Polymers18,8961
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: De novo design protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1833
Polymers18,8961
Non-polymers2872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.550, 39.340, 70.549
Angle α, β, γ (deg.)90.000, 98.807, 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: 18895.684 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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.2M MES monohydrate pH5.3, 20% w/v Polyethylene glycol 4,000

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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: 1.8→52.79 Å / Num. obs: 34581 / % possible obs: 99.1 % / Redundancy: 5.1 % / Biso Wilson estimate: 26.57 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.2
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 2006 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→33.13 Å / SU ML: 0.2225 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1701
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2169 1743 5.04 %
Rwork0.1845 32814 -
obs0.186 34557 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.18 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2567 0 30 243 2840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00372636
X-RAY DIFFRACTIONf_angle_d0.69563602
X-RAY DIFFRACTIONf_chiral_restr0.0403447
X-RAY DIFFRACTIONf_plane_restr0.0072465
X-RAY DIFFRACTIONf_dihedral_angle_d10.2024383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.36321470.3312695X-RAY DIFFRACTION99.02
1.85-1.910.26641500.27642660X-RAY DIFFRACTION98.25
1.91-1.980.28131620.21722668X-RAY DIFFRACTION98.06
1.98-2.060.25491480.1942722X-RAY DIFFRACTION99.2
2.06-2.150.2531390.19252722X-RAY DIFFRACTION99.24
2.15-2.270.20731390.18272721X-RAY DIFFRACTION99
2.27-2.410.22221160.16852750X-RAY DIFFRACTION99.17
2.41-2.60.19841820.1742720X-RAY DIFFRACTION99.18
2.6-2.860.23441700.1782710X-RAY DIFFRACTION99.34
2.86-3.270.19781320.17312786X-RAY DIFFRACTION99.56
3.27-4.120.1881370.16992782X-RAY DIFFRACTION99.62
4.12-33.130.20661210.18292878X-RAY DIFFRACTION98.94
Refinement TLS params.Method: refined / Origin x: 13.4255299013 Å / Origin y: -2.82043577541 Å / Origin z: 46.2864971138 Å
111213212223313233
T0.16218600193 Å2-0.0107694403047 Å2-0.00952335210856 Å2-0.169180992679 Å20.00195037010228 Å2--0.18347570443 Å2
L0.195160107467 °2-0.0737278266616 °2-0.0282993627389 °2-0.201079188476 °2-0.0802674412193 °2--0.519763780863 °2
S-0.00231093920163 Å °0.0111572472773 Å °0.00135964844323 Å °0.00589993105448 Å °-0.00173882254916 Å °0.0125728316282 Å °0.0300740853305 Å °-0.132447914083 Å °9.4462923657E-6 Å °
Refinement TLS groupSelection details: all

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