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- PDB-6f0s: Crystal structure of Pizza6-SYW -

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Basic information

Entry
Database: PDB / ID: 6f0s
TitleCrystal structure of Pizza6-SYW
ComponentsPizza6-SYW
KeywordsDE NOVO PROTEIN / Artificial protein / beta propeller
Function / homologyTolB, C-terminal domain / 6 Propeller / Neuraminidase / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsNoguchi, H. / De Zitter, E. / Van Meervelt, L. / Voet, A.R.D.
Funding support Belgium, 2items
OrganizationGrant numberCountry
FWOG0F9316N Belgium
FWOG051917N Belgium
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Design of tryptophan-containing mutants of the symmetrical Pizza protein for biophysical studies.
Authors: Noguchi, H. / Mylemans, B. / De Zitter, E. / Van Meervelt, L. / Tame, J.R.H. / Voet, A.
History
DepositionNov 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Pizza6-SYW


Theoretical massNumber of molelcules
Total (without water)25,7881
Polymers25,7881
Non-polymers00
Water4,450247
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 area10240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.710, 69.910, 46.940
Angle α, β, γ (deg.)90.00, 107.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pizza6-SYW


Mass: 25788.400 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.: 247 / 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: 2.05 Å3/Da / Density % sol: 39.96 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M calcium chloride, 15% (w/v) PEG6000, and 0.1 M sodium acetate pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→32.2 Å / Num. obs: 33043 / % possible obs: 99.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.055 / Net I/σ(I): 11.1
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 3.3 / Rpim(I) all: 0.298 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.5→32.197 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.84
RfactorNum. reflection% reflection
Rfree0.2037 1566 4.74 %
Rwork0.175 --
obs0.1764 33026 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→32.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 0 247 2031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082024
X-RAY DIFFRACTIONf_angle_d0.9942833
X-RAY DIFFRACTIONf_dihedral_angle_d2.9681492
X-RAY DIFFRACTIONf_chiral_restr0.064363
X-RAY DIFFRACTIONf_plane_restr0.007381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.54840.30751460.22142847X-RAY DIFFRACTION99
1.5484-1.60380.27271430.21162854X-RAY DIFFRACTION99
1.6038-1.6680.28711310.21472840X-RAY DIFFRACTION99
1.668-1.74390.21141270.21062874X-RAY DIFFRACTION99
1.7439-1.83580.27851240.20732843X-RAY DIFFRACTION99
1.8358-1.95080.21841450.19082866X-RAY DIFFRACTION99
1.9508-2.10140.22061560.1772861X-RAY DIFFRACTION100
2.1014-2.31290.22431260.18022873X-RAY DIFFRACTION99
2.3129-2.64740.21171180.17762859X-RAY DIFFRACTION98
2.6474-3.33490.20671650.17332855X-RAY DIFFRACTION99
3.3349-32.20450.14741850.13662888X-RAY DIFFRACTION100

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