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- PDB-7vty: de novo designed protein -

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Basic information

Entry
Database: PDB / ID: 7vty
Titlede novo designed protein
Componentsde novo designed protein
KeywordsDE NOVO PROTEIN
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhang, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Comput Sci / Year: 2023
Title: Rotamer-free protein sequence design based on deep learning and self-consistency.
Authors: Zhang, L.
History
DepositionOct 31, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: de novo designed protein


Theoretical massNumber of molelcules
Total (without water)10,2551
Polymers10,2551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.035, 56.035, 95.075
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein de novo designed protein


Mass: 10254.738 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)

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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: 3.64 Å3/Da / Density % sol: 66.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 4% v/v Tacsimate pH 7.0 12% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→48.27 Å / Num. obs: 4957 / % possible obs: 97 % / Redundancy: 6.1 % / Biso Wilson estimate: 68.52 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.7
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 569 / CC1/2: 0.766

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1cy5

1cy5


Resolution: 2.5→39.62 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 22.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2754 264 5.34 %
Rwork0.2235 4680 -
obs0.2262 4944 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.75 Å2 / Biso mean: 70.9146 Å2 / Biso min: 44.01 Å2
Refinement stepCycle: final / Resolution: 2.5→39.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms715 0 0 0 715
Num. residues----90
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-3.150.361460.27442368251499
3.15-39.620.25321180.2122312243095

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