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- PDB-7dgu: De novo designed protein H4A1R -

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Basic information

Entry
Database: PDB / ID: 7dgu
TitleDe novo designed protein H4A1R
Componentsde novo designed protein H4A1R
KeywordsDE NOVO PROTEIN / Designed protein
Biological speciesEscherichia coli 'BL21-GoldpLysS AG'
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsXu, Y. / Liao, S. / Chen, Q. / Liu, H.
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 1.0Nov 24, 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 H4A1R


Theoretical massNumber of molelcules
Total (without water)12,0291
Polymers12,0291
Non-polymers00
Water1,18966
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 area5640 Å2
Unit cell
Length a, b, c (Å)33.407, 33.407, 159.787
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-206-

HOH

21A-242-

HOH

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Components

#1: Protein de novo designed protein H4A1R


Mass: 12029.239 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.: 66 / 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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.0 M Potassium/sodium phosphate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.75→12.81 Å / Num. obs: 11152 / % possible obs: 99.7 % / Redundancy: 9.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.4
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 1.008 / Num. unique obs: 1073 / CC1/2: 0.588

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→12.81 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 1118 10.03 %
Rwork0.1984 10034 -
obs0.2017 11152 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.56 Å2 / Biso mean: 28.1289 Å2 / Biso min: 13.41 Å2
Refinement stepCycle: final / Resolution: 1.75→12.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms756 0 0 66 822
Biso mean---40.66 -
Num. residues----97
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.75-1.830.30841370.259712171354
1.83-1.930.27991340.264112091343
1.93-2.050.26261350.215612171352
2.05-2.20.2231360.188712531389
2.2-2.420.19611360.178312411377
2.42-2.770.2111450.19612621407
2.77-3.470.23081410.190612641405
3.48-12.810.23111540.19413711525
Refinement TLS params.Method: refined / Origin x: 2.6867 Å / Origin y: -14.1852 Å / Origin z: 12.0337 Å
111213212223313233
T0.1128 Å20.0231 Å2-0.0083 Å2-0.1216 Å20.0036 Å2--0.1418 Å2
L1.8481 °2-0.2034 °20.0797 °2-1.0565 °2-0.0861 °2--2.488 °2
S0.0263 Å °0.0597 Å °-0.0937 Å °-0.0445 Å °-0.062 Å °-0.0651 Å °0.1399 Å °0.1748 Å °-0.0013 Å °
Refinement TLS groupSelection details: all

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