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- PDB-8k7m: De novo design protein -T01 -

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Basic information

Entry
Database: PDB / ID: 8k7m
TitleDe novo design protein -T01
ComponentsDe novo design protein
KeywordsDE NOVO PROTEIN / De novo design protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 26, 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

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Assembly

Deposited unit
C: De novo design protein
B: De novo design protein
D: De novo design protein
A: De novo design protein


Theoretical massNumber of molelcules
Total (without water)102,2124
Polymers102,2124
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.653, 80.371, 78.913
Angle α, β, γ (deg.)90.00, 93.90, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.0397524431903, -0.988715503224, -0.144434749785), (-0.990268095138, -0.0582774077155, 0.126383715331), (-0.133374821505, 0.138005063078, -0.981410087351)21.8589818997, 18.080424075, 33.208076144
2given(-0.0349859897343, 0.989450647186, 0.14058235062), (0.991297086788, 0.0164945711147, 0.130606335408), (0.126909677516, 0.143928266533, -0.981416622972)13.616850216, -17.0615434187, 28.9410340647
3given(-0.999919125926, 0.0104212888607, 0.00728960528498), (-0.0120354716484, -0.960621946666, -0.277597952094), (0.00410962637337, -0.277663235454, 0.960669682382)35.4912157097, 9.83860879665, 1.47356191718

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Components

#1: Protein
De novo design protein


Mass: 25553.086 Da / Num. of mol.: 4
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.: 45 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 0.1M Sodium acetate pH4.5 20% v/v PEG Smear High

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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 PILATUS 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: 2.7→45.28 Å / Num. obs: 24681 / % possible obs: 99.77 % / Redundancy: 6.8 % / Biso Wilson estimate: 59.43 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.28
Reflection shellResolution: 2.7→2.796 Å / Num. unique obs: 2424 / CC1/2: 0.798

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→45.28 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 1280 5.19 %
Rwork0.2025 --
obs0.2053 24673 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.97 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6871 0 0 45 6916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096947
X-RAY DIFFRACTIONf_angle_d1.1389389
X-RAY DIFFRACTIONf_dihedral_angle_d12.1962619
X-RAY DIFFRACTIONf_chiral_restr0.0621171
X-RAY DIFFRACTIONf_plane_restr0.0081179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.810.36551540.32862541X-RAY DIFFRACTION100
2.81-2.940.36781460.28712590X-RAY DIFFRACTION100
2.94-3.090.3131240.24782609X-RAY DIFFRACTION100
3.09-3.280.30031680.25392561X-RAY DIFFRACTION100
3.28-3.540.34591300.25762603X-RAY DIFFRACTION100
3.54-3.890.29731170.20652630X-RAY DIFFRACTION100
3.89-4.460.23651490.17762603X-RAY DIFFRACTION100
4.46-5.610.22561620.16622595X-RAY DIFFRACTION100
5.61-45.280.17271300.1592661X-RAY DIFFRACTION99

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