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- PDB-8kc0: De novo design protein -NB8 -

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Basic information

Entry
Database: PDB / ID: 8kc0
TitleDe novo design protein -NB8
ComponentsDe novo design protein -NB8
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
DepositionAug 5, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 7, 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 -NB8


Theoretical massNumber of molelcules
Total (without water)14,2651
Polymers14,2651
Non-polymers00
Water1,09961
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)46.160, 46.160, 127.157
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein De novo design protein -NB8


Mass: 14265.160 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.: 61 / 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: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 0.8M Succinic acid pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→46.16 Å / Num. obs: 15117 / % possible obs: 99.9 % / Redundancy: 22.3 % / Biso Wilson estimate: 35.28 Å2 / CC1/2: 1 / Net I/σ(I): 24.7
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 673 / CC1/2: 0.991

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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→32.64 Å / SU ML: 0.2914 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.2762
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2745 1496 9.9 %
Rwork0.232 13621 -
obs0.2362 15117 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.15 Å2
Refinement stepCycle: LAST / Resolution: 2.1→32.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms849 0 0 61 910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044857
X-RAY DIFFRACTIONf_angle_d0.73881157
X-RAY DIFFRACTIONf_chiral_restr0.0511142
X-RAY DIFFRACTIONf_plane_restr0.0045148
X-RAY DIFFRACTIONf_dihedral_angle_d4.4348118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.170.39881350.30951191X-RAY DIFFRACTION98.08
2.17-2.250.32241350.28471249X-RAY DIFFRACTION97.33
2.25-2.340.3121260.26781231X-RAY DIFFRACTION97.77
2.34-2.440.32081270.26521197X-RAY DIFFRACTION96.08
2.44-2.570.3711340.25911262X-RAY DIFFRACTION99.5
2.57-2.730.31031430.2911246X-RAY DIFFRACTION99.71
2.73-2.940.35131380.28241239X-RAY DIFFRACTION99.78
2.94-3.240.26581410.261258X-RAY DIFFRACTION99.86
3.24-3.70.32351350.2021246X-RAY DIFFRACTION100
3.71-4.660.18121410.18041261X-RAY DIFFRACTION99.36
4.67-32.640.24031410.22151241X-RAY DIFFRACTION99.64
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)
14.853111806730.01447370148410.5490015090326.31946820978-1.749685610089.44287471127-0.509408330678-1.16593403819-0.6406997476420.1290191373450.1766831832860.2983694909021.546936542960.6572663595940.05048710593410.6196594954070.09955966959050.09958439656910.5607482253760.1094471947860.2911935715861.98361229186-26.4003262895-9.08959907758
27.982199436912.39205760115-2.340622141685.83087253926-3.873281453646.70507027505-0.1186064954160.315648977948-0.655628723416-0.5314908065620.03917230345820.1466842064321.04309919798-0.2959129846060.1086275465790.452888256169-0.0798683144916-0.02108258889290.308631884791-0.03619685847730.2599803889450.442906782344-23.0074387425-24.0786259442
32.510488268640.947325348003-3.439336990864.71449941448-0.2174015595845.351362232270.0452236613493-0.2660607534931.119872585320.4199233777530.1993625593940.673846687569-0.255528162838-1.00437202353-0.1695815394350.2957852923950.01208070541920.02838942367990.5230245528570.01919746439030.311853339125-3.20811878362-18.02700704-16.7100920434
43.8948351184-4.89531531294-1.672532077077.510975653691.383854268074.80234729276-0.411592278901-0.8204010171940.9775849583280.0808985640810.6286330346610.381727467229-0.368968143875-0.478449555549-0.286617668790.3874462655440.1243357769450.004936121713340.7475400290160.1298694387340.3427048926860.130743801355-18.8912929159-8.23448851349
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 2 through 29 )2 - 291 - 28
22chain 'A' and (resid 30 through 77 )30 - 7729 - 76
33chain 'A' and (resid 78 through 95 )78 - 9577 - 94
44chain 'A' and (resid 96 through 116 )96 - 11695 - 115

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