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- PDB-8kc8: De novo design protein -T11 -

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Basic information

Entry
Database: PDB / ID: 8kc8
TitleDe novo design protein -T11
ComponentsDe novo design protein -T11
KeywordsDE NOVO PROTEIN / De novo design protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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 6, 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 -T11


Theoretical massNumber of molelcules
Total (without water)24,1501
Polymers24,1501
Non-polymers00
Water00
1
A: De novo design protein -T11

A: De novo design protein -T11

A: De novo design protein -T11


Theoretical massNumber of molelcules
Total (without water)72,4513
Polymers72,4513
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area5070 Å2
ΔGint-29 kcal/mol
Surface area27950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.212, 150.212, 150.212
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132
Space group name HallI4bd2c3

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Components

#1: Protein De novo design protein -T11


Mass: 24150.490 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)
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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 1.8M Sodium phosphate monobasic monohydrate,Potassium phosphate dibasic ,pH8.2

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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: Jan 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.65→61.32 Å / Num. obs: 8196 / % possible obs: 94 % / Redundancy: 61.8 % / Biso Wilson estimate: 74.83 Å2 / CC1/2: 0.999 / Net I/σ(I): 35
Reflection shellResolution: 2.65→2.8 Å / Num. unique obs: 1007 / CC1/2: 0.805

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→47.5 Å / SU ML: 0.391 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.7592
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2553 818 10 %
Rwork0.2214 7360 -
obs0.2247 8178 94.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.88 Å2
Refinement stepCycle: LAST / Resolution: 2.65→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 0 0 1612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00371631
X-RAY DIFFRACTIONf_angle_d0.61662227
X-RAY DIFFRACTIONf_chiral_restr0.0383279
X-RAY DIFFRACTIONf_plane_restr0.0047295
X-RAY DIFFRACTIONf_dihedral_angle_d4.6939238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.820.35051170.31231048X-RAY DIFFRACTION82.74
2.82-3.040.36541420.31671281X-RAY DIFFRACTION99.93
3.04-3.340.28561420.27441279X-RAY DIFFRACTION99.93
3.34-3.830.31111260.26271127X-RAY DIFFRACTION87.2
3.83-4.820.231360.18731232X-RAY DIFFRACTION94.09
4.82-47.50.21591550.1931393X-RAY DIFFRACTION99.87
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)
11.685721287970.185876744805-0.0565713238070.07045763865180.1424057912810.506627524050.0126108079498-0.5909325237440.131390834960.1762089664750.07810019176730.00447772698062-0.1759061745930.553849070628-0.0001685181205240.5444180017870.01290619427910.02904069480920.567167881971-0.06735400678610.45472646526414.676241263-6.09703298622-6.50258664822
21.77669407976-0.940005365647-0.5884052615662.160068647510.2419312533523.1099684626-0.1897866849890.0648567659350.079859788749-0.258782102892-0.05495905587510.149095551572-0.0904041063411-0.3798780891349.32974803907E-50.4376201734860.01935662900140.007541523280810.522083987548-0.01096394652120.4380830569719.47918874955-8.49133317766-22.7859450697
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 1 through 88 )1 - 881 - 88
22chain 'A' and (resid 89 through 227 )89 - 22789 - 227

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