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- PDB-6mrr: De novo designed protein Foldit1 -

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Basic information

Entry
Database: PDB / ID: 6mrr
TitleDe novo designed protein Foldit1
ComponentsFoldit1
KeywordsDE NOVO PROTEIN / Foldit
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsKoepnick, B. / Bick, M.J. / Estep, R.D. / Kleinfelter, S. / Wei, L. / 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: Foldit1


Theoretical massNumber of molelcules
Total (without water)8,1581
Polymers8,1581
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Protein elutes as a monodisperse peak at the expected volume
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.045, 43.584, 29.276
Angle α, β, γ (deg.)90.00, 99.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Foldit1


Mass: 8158.348 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 1.86 Å3/Da / Density % sol: 33.77 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M potassium chloride, 0.05 M HEPES, pH 7.5, 35% v/v pentaerythritol propoxylate (5/4 PO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2017
RadiationMonochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.07→43.58 Å / Num. obs: 22566 / % possible obs: 85.3 % / Redundancy: 3.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.026 / Rpim(I) all: 0.017 / Rrim(I) all: 0.031 / Net I/σ(I): 18.9
Reflection shellResolution: 1.07→1.09 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 430 / CC1/2: 0.981 / Rpim(I) all: 0.131 / Rrim(I) all: 0.221 / % possible all: 32.8

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Processing

Software
NameVersionClassification
PHENIX(dev_3112: ???)refinement
XDSJun 17, 2015data reduction
XDSJun 17, 2015data scaling
PHASER2.8.2.phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational design generated by Foldit software

Resolution: 1.18→28.916 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.42
RfactorNum. reflection% reflection
Rfree0.1819 1829 10.01 %
Rwork0.1464 --
obs0.1499 18279 92.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.18→28.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms551 0 0 116 667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008582
X-RAY DIFFRACTIONf_angle_d0.833781
X-RAY DIFFRACTIONf_dihedral_angle_d18.886232
X-RAY DIFFRACTIONf_chiral_restr0.07586
X-RAY DIFFRACTIONf_plane_restr0.004102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1801-1.2120.17121340.12961220X-RAY DIFFRACTION88
1.212-1.24760.21071320.12891189X-RAY DIFFRACTION88
1.2476-1.28790.19531350.13691219X-RAY DIFFRACTION90
1.2879-1.33390.17031410.13151253X-RAY DIFFRACTION91
1.3339-1.38730.17371390.13241237X-RAY DIFFRACTION92
1.3873-1.45050.19181390.12321252X-RAY DIFFRACTION92
1.4505-1.52690.15631370.11781243X-RAY DIFFRACTION93
1.5269-1.62260.14921440.12421290X-RAY DIFFRACTION94
1.6226-1.74790.16251410.12551280X-RAY DIFFRACTION94
1.7479-1.92370.17341440.14091288X-RAY DIFFRACTION95
1.9237-2.2020.14021450.12541300X-RAY DIFFRACTION95
2.202-2.77390.18381450.15981315X-RAY DIFFRACTION96
2.7739-28.92440.21441530.17191364X-RAY DIFFRACTION97

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