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- PDB-6f0t: Crystal structure of Pizza6-SFW -

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Basic information

Entry
Database: PDB / ID: 6f0t
TitleCrystal structure of Pizza6-SFW
ComponentsPizza6-SFW
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: 1.74 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-SFW
B: Pizza6-SFW
C: Pizza6-SFW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6935
Polymers77,5093
Non-polymers1842
Water7,044391
1
A: Pizza6-SFW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0213
Polymers25,8361
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pizza6-SFW


Theoretical massNumber of molelcules
Total (without water)25,8361
Polymers25,8361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pizza6-SFW


Theoretical massNumber of molelcules
Total (without water)25,8361
Polymers25,8361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.529, 69.454, 78.710
Angle α, β, γ (deg.)65.36, 89.80, 77.16
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Pizza6-SFW


Mass: 25836.400 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.25 M calcium chloride 15% (w/v) PEG6000, and 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.74→38.93 Å / Num. obs: 61581 / % possible obs: 98.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.043 / Net I/σ(I): 11.4
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.635 / Rpim(I) all: 0.499 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.74→38.93 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.24
RfactorNum. reflection% reflection
Rfree0.2333 2975 4.85 %
Rwork0.1924 --
obs0.1945 61308 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.74→38.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5361 0 12 391 5764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065526
X-RAY DIFFRACTIONf_angle_d0.8427633
X-RAY DIFFRACTIONf_dihedral_angle_d2.8764202
X-RAY DIFFRACTIONf_chiral_restr0.056967
X-RAY DIFFRACTIONf_plane_restr0.0051001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.76850.38051290.32822732X-RAY DIFFRACTION97
1.7685-1.7990.40811320.31072806X-RAY DIFFRACTION98
1.799-1.83170.36221290.28652789X-RAY DIFFRACTION98
1.8317-1.8670.35461240.27642739X-RAY DIFFRACTION98
1.867-1.90510.31861460.26232805X-RAY DIFFRACTION98
1.9051-1.94650.31661450.24822721X-RAY DIFFRACTION98
1.9465-1.99180.30381360.24152804X-RAY DIFFRACTION98
1.9918-2.04160.29861360.23482796X-RAY DIFFRACTION98
2.0416-2.09680.30051330.23522728X-RAY DIFFRACTION98
2.0968-2.15850.29141600.23162790X-RAY DIFFRACTION99
2.1585-2.22810.28591560.22182773X-RAY DIFFRACTION99
2.2281-2.30780.29121480.21072822X-RAY DIFFRACTION98
2.3078-2.40020.23161080.21392757X-RAY DIFFRACTION99
2.4002-2.50940.27261300.22412868X-RAY DIFFRACTION99
2.5094-2.64160.29691290.21762747X-RAY DIFFRACTION99
2.6416-2.80710.24851490.2152793X-RAY DIFFRACTION99
2.8071-3.02380.23071540.20812801X-RAY DIFFRACTION99
3.0238-3.32790.22321340.18822787X-RAY DIFFRACTION99
3.3279-3.80910.22571620.16932760X-RAY DIFFRACTION99
3.8091-4.79770.18691660.13162767X-RAY DIFFRACTION99
4.7977-38.93980.15421690.14382748X-RAY DIFFRACTION98

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