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- PDB-6rli: The structure of the self-assembled 3fPizza6-SH crystal -

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Basic information

Entry
Database: PDB / ID: 6rli
TitleThe structure of the self-assembled 3fPizza6-SH crystal
Components3fPizza6-SH
KeywordsDE NOVO PROTEIN / Pizza / beta-propeller / de novo / artificial protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsNoguchi, H. / Voet, A.R.D.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - FlandersG0E4717N, G0F9316N, G051917N Belgium
CitationJournal: To Be Published
Title: Self-assembled Pizza proteins
Authors: Noguchi, H. / Voet, A.R.D.
History
DepositionMay 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3fPizza6-SH


Theoretical massNumber of molelcules
Total (without water)25,8731
Polymers25,8731
Non-polymers00
Water7,800433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.029, 42.114, 42.194
Angle α, β, γ (deg.)100.57, 100.41, 100.07
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 3fPizza6-SH


Mass: 25872.500 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.: 433 / 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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: 20mM HEPES pH8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.15→40.46 Å / Num. obs: 13784 / % possible obs: 87.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 9.88 Å2 / Net I/σ(I): 10.6
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 4510 / Rpim(I) all: 0.175 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ww9

3ww9


Resolution: 1.15→40.46 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.92
RfactorNum. reflection% reflection
Rfree0.216 4606 4.85 %
Rwork0.2007 --
obs0.2015 94873 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.15→40.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 0 433 2217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051864
X-RAY DIFFRACTIONf_angle_d0.7782578
X-RAY DIFFRACTIONf_dihedral_angle_d13.192623
X-RAY DIFFRACTIONf_chiral_restr0.079329
X-RAY DIFFRACTIONf_plane_restr0.006342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.16310.21581570.18842790X-RAY DIFFRACTION92
1.1631-1.17680.22021230.18783017X-RAY DIFFRACTION96
1.1768-1.19110.25081310.18412951X-RAY DIFFRACTION96
1.1911-1.20620.17341980.16682950X-RAY DIFFRACTION97
1.2062-1.22210.17421470.16312971X-RAY DIFFRACTION97
1.2221-1.23880.21311320.17183047X-RAY DIFFRACTION97
1.2388-1.25650.23182000.17412869X-RAY DIFFRACTION97
1.2565-1.27530.22191990.18173000X-RAY DIFFRACTION97
1.2753-1.29520.21861810.17872949X-RAY DIFFRACTION97
1.2952-1.31640.18241290.18033074X-RAY DIFFRACTION97
1.3164-1.33910.22311480.1762924X-RAY DIFFRACTION98
1.3391-1.36350.23861240.18193073X-RAY DIFFRACTION97
1.3635-1.38970.19071240.18783014X-RAY DIFFRACTION98
1.3897-1.41810.25481090.19093074X-RAY DIFFRACTION98
1.4181-1.44890.21171330.1823047X-RAY DIFFRACTION98
1.4489-1.48260.17641260.18383003X-RAY DIFFRACTION98
1.4826-1.51970.17381060.18783035X-RAY DIFFRACTION98
1.5197-1.56080.18491710.18863030X-RAY DIFFRACTION98
1.5608-1.60670.2197860.19043076X-RAY DIFFRACTION98
1.6067-1.65860.22781610.19433005X-RAY DIFFRACTION98
1.6586-1.71790.21512150.20332954X-RAY DIFFRACTION98
1.7179-1.78660.23371640.21963041X-RAY DIFFRACTION99
1.7866-1.8680.26491590.21833048X-RAY DIFFRACTION99
1.868-1.96640.22031520.21563063X-RAY DIFFRACTION99
1.9664-2.08960.20371370.20333079X-RAY DIFFRACTION99
2.0896-2.2510.20652020.20392992X-RAY DIFFRACTION99
2.251-2.47750.21361650.21543090X-RAY DIFFRACTION99
2.4775-2.83590.24371280.22253053X-RAY DIFFRACTION100
2.8359-3.57260.21942190.21043009X-RAY DIFFRACTION100
3.5726-40.48710.2091800.19313039X-RAY DIFFRACTION99

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