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- PDB-7dgy: De novo designed protein H4C2R -

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Basic information

Entry
Database: PDB / ID: 7dgy
TitleDe novo designed protein H4C2R
Componentsde novo designed protein H4C2R
KeywordsDE NOVO PROTEIN / Designed protein
Biological speciesEscherichia coli 'BL21-GoldpLysS AG'
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsXu, Y. / Liao, S. / Chen, Q. / Liu, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2022
Title: A backbone-centred energy function of neural networks for protein design.
Authors: Huang, B. / Xu, Y. / Hu, X. / Liu, Y. / Liao, S. / Zhang, J. / Huang, C. / Hong, J. / Chen, Q. / Liu, H.
History
DepositionNov 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 23, 2022Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / struct
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _entity.pdbx_description / _struct.title
Revision 1.3Mar 2, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: de novo designed protein H4C2R


Theoretical massNumber of molelcules
Total (without water)11,6561
Polymers11,6561
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5590 Å2
Unit cell
Length a, b, c (Å)70.682, 70.682, 64.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-270-

HOH

21A-280-

HOH

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Components

#1: Protein de novo designed protein H4C2R


Mass: 11655.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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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: 3.46 Å3/Da / Density % sol: 64.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.1 M Ammonium tartrate dibasic, 0.1 M sodium acetate trihydrate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.8→49.98 Å / Num. obs: 15624 / % possible obs: 100 % / Redundancy: 25.3 % / CC1/2: 1 / Rmerge(I) obs: 0.043 / Net I/σ(I): 45
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 1520 / CC1/2: 0.943

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.66 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1925 1563 10 %
Rwork0.1762 14061 -
obs0.1778 15624 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.75 Å2 / Biso mean: 35.503 Å2 / Biso min: 22.15 Å2
Refinement stepCycle: final / Resolution: 1.8→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms766 0 0 81 847
Biso mean---48.31 -
Num. residues----99
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.860.23661390.189712531392
1.86-1.930.22531370.177812381375
1.93-20.2511400.182912531393
2-2.10.17091400.170612511391
2.1-2.210.17191380.161812601398
2.21-2.340.19091420.161112701412
2.34-2.530.21461420.18112691411
2.53-2.780.21421400.179512711411
2.78-3.180.19191430.182212881431
3.18-4.010.18281460.170813111457
4.01-47.660.18341560.180113971553
Refinement TLS params.Method: refined / Origin x: -7.1633 Å / Origin y: 22.8074 Å / Origin z: -15.5066 Å
111213212223313233
T0.2337 Å20.0196 Å20.0045 Å2-0.2447 Å20.0029 Å2--0.2656 Å2
L1.4347 °20.6747 °20.2141 °2-1.48 °2-0.2319 °2--0.2118 °2
S-0.0615 Å °-0.0896 Å °-0.0054 Å °-0.0733 Å °0.0012 Å °-0.1414 Å °0.0138 Å °-0.0105 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 98
2X-RAY DIFFRACTION1allS1 - 85

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