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- PDB-7vu4: de novo design based on 1r26 -

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Basic information

Entry
Database: PDB / ID: 7vu4
Titlede novo design based on 1r26
Componentsde novo design protein
KeywordsDE NOVO PROTEIN
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.7 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
DepositionNov 1, 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 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: de novo design protein


Theoretical massNumber of molelcules
Total (without water)13,7971
Polymers13,7971
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.772, 52.651, 67.192
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein de novo design protein


Mass: 13796.659 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.: 73 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.72 Å3/Da / Density % sol: 28.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium cacodylate pH6.5 27 % w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 1.7→41.44 Å / Num. obs: 11028 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 20.95 Å2 / CC1/2: 0.999 / Net I/σ(I): 21.6
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 560 / CC1/2: 0.915

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.7→24.87 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2254 540 4.92 %
Rwork0.1916 10443 -
obs0.1932 10983 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.39 Å2 / Biso mean: 31.9811 Å2 / Biso min: 11.59 Å2
Refinement stepCycle: final / Resolution: 1.7→24.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 0 73 1004
Biso mean---34.7 -
Num. residues----117
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.870.27531270.21525582685
1.87-2.140.22461340.190625582692
2.14-2.70.22961530.189825892742
2.7-24.870.21521260.189127382864
Refinement TLS params.Method: refined / Origin x: -8.1011 Å / Origin y: 26.9888 Å / Origin z: 17.7763 Å
111213212223313233
T0.1401 Å2-0.0027 Å20.0047 Å2-0.1269 Å20.0055 Å2--0.1447 Å2
L1.417 °2-0.1338 °2-0.0243 °2-0.9612 °2-0.022 °2--1.076 °2
S0.0109 Å °-0.0003 Å °-0.077 Å °-0.0595 Å °0.0058 Å °0.0091 Å °0.0639 Å °-0.0483 Å °0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 117
2X-RAY DIFFRACTION1allS1 - 75

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