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- PDB-6wi5: De novo designed protein Foldit4 -

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Basic information

Entry
Database: PDB / ID: 6wi5
TitleDe novo designed protein Foldit4
ComponentsDe novo designed protein Foldit4
KeywordsDE NOVO PROTEIN / Foldit / de novo design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsBera, A.K. / Koepnick, B. / Boykov, A. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2020
Title: De novo design of protein logic gates.
Authors: Chen, Z. / Kibler, R.D. / Hunt, A. / Busch, F. / Pearl, J. / Jia, M. / VanAernum, Z.L. / Wicky, B.I.M. / Dods, G. / Liao, H. / Wilken, M.S. / Ciarlo, C. / Green, S. / El-Samad, H. / ...Authors: Chen, Z. / Kibler, R.D. / Hunt, A. / Busch, F. / Pearl, J. / Jia, M. / VanAernum, Z.L. / Wicky, B.I.M. / Dods, G. / Liao, H. / Wilken, M.S. / Ciarlo, C. / Green, S. / El-Samad, H. / Stamatoyannopoulos, J. / Wysocki, V.H. / Jewett, M.C. / Boyken, S.E. / Baker, D.
History
DepositionApr 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.2Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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

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Assembly

Deposited unit
A: De novo designed protein Foldit4
B: De novo designed protein Foldit4


Theoretical massNumber of molelcules
Total (without water)22,0632
Polymers22,0632
Non-polymers00
Water1,820101
1
A: De novo designed protein Foldit4


Theoretical massNumber of molelcules
Total (without water)11,0321
Polymers11,0321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: De novo designed protein Foldit4


Theoretical massNumber of molelcules
Total (without water)11,0321
Polymers11,0321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.027, 64.027, 221.412
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein De novo designed protein Foldit4


Mass: 11031.742 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DE NOVO DESIGNED / Source: (synth.) synthetic construct (others)
#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: 52.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.09 MNPS, 0.1 M Sodium HEPES; MOPS, pH 7.5 and 30% P500MME_P20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99993 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99993 Å / Relative weight: 1
ReflectionResolution: 1.83→48.4 Å / Num. obs: 20876 / % possible obs: 99.7 % / Redundancy: 9.5 % / Biso Wilson estimate: 32.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.2
Reflection shellResolution: 1.83→1.88 Å / Redundancy: 9.8 % / Rmerge(I) obs: 2.917 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1508 / CC1/2: 0.766 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18rc2_3793refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Designed Model

Resolution: 1.83→48.36 Å / SU ML: 0.273 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.6529
RfactorNum. reflection% reflection
Rfree0.2713 998 4.79 %
Rwork0.2474 --
obs0.2486 20829 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.54 Å2
Refinement stepCycle: LAST / Resolution: 1.83→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1457 0 0 107 1564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00141486
X-RAY DIFFRACTIONf_angle_d0.33411999
X-RAY DIFFRACTIONf_chiral_restr0.0446249
X-RAY DIFFRACTIONf_plane_restr0.001257
X-RAY DIFFRACTIONf_dihedral_angle_d27.3205599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.920.45811460.3832670X-RAY DIFFRACTION95.91
1.92-2.040.32221450.31232780X-RAY DIFFRACTION99.69
2.04-2.20.33511360.28962832X-RAY DIFFRACTION99.9
2.2-2.420.29161380.2632827X-RAY DIFFRACTION99.93
2.42-2.770.28751430.26772862X-RAY DIFFRACTION100
2.77-3.490.25821450.24572894X-RAY DIFFRACTION100
3.49-48.360.23651450.21342966X-RAY DIFFRACTION97.13

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