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- PDB-6d0t: De novo design of a fluorescence-activating beta barrel - BB1 -

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Basic information

Entry
Database: PDB / ID: 6d0t
TitleDe novo design of a fluorescence-activating beta barrel - BB1
ComponentsBB1
KeywordsDE NOVO PROTEIN / beta-barrel / design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsDou, J. / Vorobieva, A.A. / Sheffler, W. / Doyle, L.A. / Park, H. / Bick, M.J. / Mao, B. / Foight, G.W. / Lee, M. / Carter, L. ...Dou, J. / Vorobieva, A.A. / Sheffler, W. / Doyle, L.A. / Park, H. / Bick, M.J. / Mao, B. / Foight, G.W. / Lee, M. / Carter, L. / Sankaran, B. / Ovchinnikov, S. / Marcos, E. / Huang, P. / Vaughan, J.C. / Stoddard, B.L. / Baker, D.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
National Science Foundation (NSF, United States)CHE1332907 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2018
Title: De novo design of a fluorescence-activating beta-barrel.
Authors: Dou, J. / Vorobieva, A.A. / Sheffler, W. / Doyle, L.A. / Park, H. / Bick, M.J. / Mao, B. / Foight, G.W. / Lee, M.Y. / Gagnon, L.A. / Carter, L. / Sankaran, B. / Ovchinnikov, S. / Marcos, E. ...Authors: Dou, J. / Vorobieva, A.A. / Sheffler, W. / Doyle, L.A. / Park, H. / Bick, M.J. / Mao, B. / Foight, G.W. / Lee, M.Y. / Gagnon, L.A. / Carter, L. / Sankaran, B. / Ovchinnikov, S. / Marcos, E. / Huang, P.S. / Vaughan, J.C. / Stoddard, B.L. / Baker, D.
History
DepositionApr 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 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 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BB1
B: BB1


Theoretical massNumber of molelcules
Total (without water)28,1312
Polymers28,1312
Non-polymers00
Water1,820101
1
A: BB1


Theoretical massNumber of molelcules
Total (without water)14,0651
Polymers14,0651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BB1


Theoretical massNumber of molelcules
Total (without water)14,0651
Polymers14,0651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.760, 32.270, 81.650
Angle α, β, γ (deg.)90.00, 100.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BB1


Mass: 14065.296 Da / Num. of mol.: 2
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.: 101 / 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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M Bis-Tris pH 5.0, 2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen stream
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2015
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.63→27.81 Å / Num. obs: 36159 / % possible obs: 99.8 % / Redundancy: 4 % / Biso Wilson estimate: 17.905 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.038 / Rrim(I) all: 0.077 / Net I/σ(I): 13.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
7.29-27.813.70.02435.54530.9980.0160.03198.6
1.63-1.674.10.6531.926480.6610.4330.88499.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia20.3.8.0data reduction
xia20.3.8.0data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computationally Designed Model

Resolution: 1.63→27.807 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.38
Details: Iterative rounds of manual model building in Coot followed by refinement in Phenix with the addition of riding hydrogen atoms, optimization of the X-ray to stereochemical and ADP weights.
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1806 5 %Random selection
Rwork0.1515 ---
obs0.1531 36147 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29 Å2
Refinement stepCycle: LAST / Resolution: 1.63→27.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1709 0 0 101 1810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011947
X-RAY DIFFRACTIONf_angle_d1.0592639
X-RAY DIFFRACTIONf_dihedral_angle_d15.721188
X-RAY DIFFRACTIONf_chiral_restr0.065256
X-RAY DIFFRACTIONf_plane_restr0.007364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.67410.26921370.21792612X-RAY DIFFRACTION100
1.6741-1.72340.25531360.19822585X-RAY DIFFRACTION99
1.7234-1.7790.26681300.17322653X-RAY DIFFRACTION100
1.779-1.84250.19791610.15942591X-RAY DIFFRACTION100
1.8425-1.91630.19151280.14182614X-RAY DIFFRACTION100
1.9163-2.00350.17331130.12562643X-RAY DIFFRACTION100
2.0035-2.10910.18261390.12232625X-RAY DIFFRACTION100
2.1091-2.24120.16731270.12922642X-RAY DIFFRACTION100
2.2412-2.41410.18291500.13342616X-RAY DIFFRACTION100
2.4141-2.65690.17811350.14692687X-RAY DIFFRACTION100
2.6569-3.0410.18211410.14532635X-RAY DIFFRACTION100
3.041-3.82970.16041500.14852673X-RAY DIFFRACTION100
3.8297-27.81110.18031590.17122765X-RAY DIFFRACTION100

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