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- PDB-8k8i: De novo design protein -N14 -

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Basic information

Entry
Database: PDB / ID: 8k8i
TitleDe novo design protein -N14
ComponentsDe novo design protein -N14
KeywordsDE NOVO PROTEIN / De novo design protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 30, 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

Downloads & links

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Assembly

Deposited unit
A: De novo design protein -N14


Theoretical massNumber of molelcules
Total (without water)20,3771
Polymers20,3771
Non-polymers00
Water61334
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)56.019, 56.019, 110.446
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein De novo design protein -N14


Mass: 20377.281 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.: 34 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.2M Ammonium sulfate 0.1M Tris pH8.0 20% v/v PEG Smear Broad

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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: 2.1→48.51 Å / Num. obs: 12192 / % possible obs: 99.7 % / Redundancy: 19.3 % / Biso Wilson estimate: 37.12 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.5
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 973 / CC1/2: 0.92

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.33 Å / SU ML: 0.2713 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2703 595 4.9 %
Rwork0.2397 11556 -
obs0.2412 12151 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.47 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1357 0 0 34 1391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00261375
X-RAY DIFFRACTIONf_angle_d0.51621893
X-RAY DIFFRACTIONf_chiral_restr0.0374247
X-RAY DIFFRACTIONf_plane_restr0.0052251
X-RAY DIFFRACTIONf_dihedral_angle_d3.7476217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.310.34531590.31142800X-RAY DIFFRACTION98.73
2.31-2.650.33991640.25912818X-RAY DIFFRACTION99.07
2.65-3.330.29481360.27632887X-RAY DIFFRACTION99.51
3.33-29.330.22491360.20763051X-RAY DIFFRACTION99.66
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.322765257360.1087789875440.1965236187251.309450853370.197737565843.953157640210.60556293972-0.5498494975870.2997875674810.614957818611-0.2304944677580.38586628092-0.40446252076-0.8697492472940.09288688924710.784801605518-0.1855380498310.1625261261020.42375621855-0.063003719760.314385241977-29.587248005713.857129064413.4780080268
23.335772163510.731201391767-1.087302419464.383002754761.697124055973.740743243760.464148822673-0.214903157299-0.3313671533450.545613307295-0.308488552196-0.2493566491560.2026693179720.173044781569-0.1511766302250.469510124105-0.108039063688-0.07129469425060.2087049412960.01443608181990.239791050258-20.95398755127.231138547517.06571127839
32.45483798698-3.108468309012.23981499326.71181369543-3.053776566715.71981259229-0.0705048100765-0.2108672938930.1765291872390.2839708414930.05227940678190.113440239021-1.03268758926-0.6067685721240.0537583130970.657487179324-0.062706328010.03679943774910.419496059235-0.07199307487350.313153911756-28.531317204513.568633937-5.49713300105
41.335979768412.9727150921.917078632679.332676271474.827015475317.42023899106-0.3436514188940.373998906419-0.709686120335-1.67244793110.418956851049-0.939856246306-0.218855914133-0.0701958900029-0.02508778257920.577046318749-0.181424529530.07800835184240.5801486438360.004680550813610.519981035055-16.06375092134.38937299935-1.28809964655
51.674272252890.664934041506-1.896815005766.03377695718-1.560306748914.028792541960.210384601419-0.454484533502-0.3855715772651.09127138727-0.113869635312-0.9109201422670.6399703852580.528248877564-0.04546031408660.808634180236-0.11648075533-0.245820979050.3521844382660.02127689152650.434763535932-14.60003903056.2456929592114.0391787574
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 48 through 139 )48 - 13949 - 140
22chain 'A' and (resid 140 through 180 )140 - 180141 - 181
33chain 'A' and (resid 181 through 210 )181 - 210182 - 211
44chain 'A' and (resid 0 through 19 )0 - 191 - 20
55chain 'A' and (resid 20 through 47 )20 - 4721 - 48

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