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- PDB-6mrs: De novo designed protein Peak6 -

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Basic information

Entry
Database: PDB / ID: 6mrs
TitleDe novo designed protein Peak6
ComponentsPeak6
KeywordsDE NOVO PROTEIN / Foldit
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.541 Å
AuthorsKoepnick, B. / Boykov, A. / Baker, D.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Science Foundation (NSF, United States)DGE-1256082 United States
CitationJournal: Nature / Year: 2019
Title: De novo protein design by citizen scientists.
Authors: Koepnick, B. / Flatten, J. / Husain, T. / Ford, A. / Silva, D.A. / Bick, M.J. / Bauer, A. / Liu, G. / Ishida, Y. / Boykov, A. / Estep, R.D. / Kleinfelter, S. / Norgard-Solano, T. / Wei, L. / ...Authors: Koepnick, B. / Flatten, J. / Husain, T. / Ford, A. / Silva, D.A. / Bick, M.J. / Bauer, A. / Liu, G. / Ishida, Y. / Boykov, A. / Estep, R.D. / Kleinfelter, S. / Norgard-Solano, T. / Wei, L. / Players, F. / Montelione, G.T. / DiMaio, F. / Popovic, Z. / Khatib, F. / Cooper, S. / Baker, D.
History
DepositionOct 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: 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_PubMed / _citation.title / _citation.year
Revision 1.2Jun 26, 2019Group: 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: Peak6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1345
Polymers8,7501
Non-polymers3844
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Protein elutes as a monodisperse peak at the expected volume.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-38 kcal/mol
Surface area4820 Å2
Unit cell
Length a, b, c (Å)52.414, 52.414, 56.086
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-103-

SO4

21A-103-

SO4

31A-285-

HOH

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Components

#1: Protein Peak6


Mass: 8749.917 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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.54 Å3/Da / Density % sol: 51.61 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999989 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2018
RadiationMonochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999989 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 12877 / % possible obs: 94.8 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.028 / Rrim(I) all: 0.092 / Χ2: 0.987 / Net I/σ(I): 27.2
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 1 / Num. unique obs: 390 / CC1/2: 0.73 / Rpim(I) all: 0.4 / Rrim(I) all: 0.917 / Χ2: 0.43 / % possible all: 58.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000v715data reduction
HKL-2000v715data scaling
PHASER2.8.2.phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational model generated by FoldIt software

Resolution: 1.541→35.284 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.88
RfactorNum. reflection% reflection
Rfree0.1975 1282 9.97 %
Rwork0.1682 --
obs0.1713 12860 94.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.541→35.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms599 0 20 89 708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006668
X-RAY DIFFRACTIONf_angle_d0.669905
X-RAY DIFFRACTIONf_dihedral_angle_d17.093419
X-RAY DIFFRACTIONf_chiral_restr0.051105
X-RAY DIFFRACTIONf_plane_restr0.003116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5408-1.60250.2881960.2756890X-RAY DIFFRACTION67
1.6025-1.67540.21881420.23561268X-RAY DIFFRACTION96
1.6754-1.76380.21481390.191298X-RAY DIFFRACTION98
1.7638-1.87430.19431480.18381337X-RAY DIFFRACTION98
1.8743-2.0190.2161470.17381319X-RAY DIFFRACTION98
2.019-2.22210.18771440.1511321X-RAY DIFFRACTION99
2.2221-2.54360.15711490.14791343X-RAY DIFFRACTION99
2.5436-3.20430.19131520.16441367X-RAY DIFFRACTION99
3.2043-35.29320.20541650.16291435X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0423-2.5988-0.47327.42670.84322.3467-0.16650.11860.1775-0.30690.08430.0857-0.23170.1714-0.00910.2038-0.039-0.03520.19560.02740.1539-19.554723.1687-9.2975
22.7793-1.30960.88562.9191-0.66191.62190.01170.17750.0956-0.1873-0.1194-0.03860.0225-0.0138-0.02920.14850.0148-0.00780.1129-0.01270.1107-24.510614.314-9.4507
31.62040.91710.81392.8887-0.2490.86470.00090.02850.109-0.0429-0.0625-0.0143-0.00880.0355-0.00670.1353-0.01740.01270.1174-0.00710.1052-21.391617.8415-0.11
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 75 )

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