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- PDB-6x9z: De novo design of transmembrane beta-barrels -

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Basic information

Entry
Database: PDB / ID: 6x9z
TitleDe novo design of transmembrane beta-barrels
ComponentsTransmembrane beta-barrels
KeywordsDE NOVO PROTEIN / transmembrane beta-barrels / de novo design
Function / homologyPorin - #20 / Porin / Beta Barrel / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBera, A.K. / Vorobieva, A.A. / Kang, A.S. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2021
Title: De novo design of transmembrane beta barrels.
Authors: Vorobieva, A.A. / White, P. / Liang, B. / Horne, J.E. / Bera, A.K. / Chow, C.M. / Gerben, S. / Marx, S. / Kang, A. / Stiving, A.Q. / Harvey, S.R. / Marx, D.C. / Khan, G.N. / Fleming, K.G. / ...Authors: Vorobieva, A.A. / White, P. / Liang, B. / Horne, J.E. / Bera, A.K. / Chow, C.M. / Gerben, S. / Marx, S. / Kang, A. / Stiving, A.Q. / Harvey, S.R. / Marx, D.C. / Khan, G.N. / Fleming, K.G. / Wysocki, V.H. / Brockwell, D.J. / Tamm, L.K. / Radford, S.E. / Baker, D.
History
DepositionJun 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transmembrane beta-barrels


Theoretical massNumber of molelcules
Total (without water)13,4241
Polymers13,4241
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.083, 51.083, 116.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-224-

HOH

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Components

#1: Protein Transmembrane beta-barrels


Mass: 13424.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Tris pH 8.5 and 10% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.05→41.37 Å / Num. obs: 7132 / % possible obs: 99.54 % / Redundancy: 7.9 % / Biso Wilson estimate: 32.25 Å2 / CC1/2: 0.995 / CC star: 0.999 / Net I/σ(I): 6.66
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1.18 / Num. unique obs: 735 / CC1/2: 0.689 / CC star: 0.903 / % possible all: 98.13

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Designed model

Resolution: 2.05→41.37 Å / SU ML: 0.2553 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 34.2737
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2736 389 5.47 %
Rwork0.2603 6725 -
obs0.2611 7114 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.28 Å2
Refinement stepCycle: LAST / Resolution: 2.05→41.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms909 0 0 31 940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032941
X-RAY DIFFRACTIONf_angle_d0.61821289
X-RAY DIFFRACTIONf_chiral_restr0.0501145
X-RAY DIFFRACTIONf_plane_restr0.0068164
X-RAY DIFFRACTIONf_dihedral_angle_d14.1304326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.120.29331260.2862260X-RAY DIFFRACTION99.38
2.35-2.960.33841260.31162227X-RAY DIFFRACTION99.49
2.96-41.370.24971370.2372238X-RAY DIFFRACTION99.75

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