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- PDB-6f0q: Crystal structure of Pizza6-AYW -

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Basic information

Entry
Database: PDB / ID: 6f0q
TitleCrystal structure of Pizza6-AYW
ComponentsPizza6-AYW
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 / MOLECULAR REPLACEMENT / Resolution: 1.3 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 1.1Jan 17, 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: Pizza6-AYW
B: Pizza6-AYW


Theoretical massNumber of molelcules
Total (without water)51,7152
Polymers51,7152
Non-polymers00
Water11,944663
1
A: Pizza6-AYW


Theoretical massNumber of molelcules
Total (without water)25,8581
Polymers25,8581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pizza6-AYW


Theoretical massNumber of molelcules
Total (without water)25,8581
Polymers25,8581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.010, 70.350, 58.210
Angle α, β, γ (deg.)90.00, 100.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pizza6-AYW


Mass: 25857.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-28b / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 663 / 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: 33.99 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MIB (Mixtures of sodium malonate, imidazole, boric acid in the molar rations 2:3:3 buffer) or MMT (Mixtures of DL-malic acid, MES and Tris base in the molar rations 1:2:2 buffer) pH 5.0, 30% (w/v) PEG1500

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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: 1.3→26.501 Å / Num. obs: 86627 / % possible obs: 94.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.062 / Net I/σ(I): 8.2
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.8 / Rpim(I) all: 0.301 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WW9

3ww9


Resolution: 1.3→26.501 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.192 4205 4.86 %
Rwork0.1553 --
obs0.1571 86544 94.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→26.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3580 0 0 663 4243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164058
X-RAY DIFFRACTIONf_angle_d1.4845682
X-RAY DIFFRACTIONf_dihedral_angle_d4.0021982
X-RAY DIFFRACTIONf_chiral_restr0.156723
X-RAY DIFFRACTIONf_plane_restr0.011760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.27761270.21522665X-RAY DIFFRACTION93
1.3148-1.33020.25651430.20022679X-RAY DIFFRACTION92
1.3302-1.34650.23741320.18822716X-RAY DIFFRACTION93
1.3465-1.36350.25061300.18932635X-RAY DIFFRACTION92
1.3635-1.38140.23741430.18852681X-RAY DIFFRACTION92
1.3814-1.40040.23641330.17592648X-RAY DIFFRACTION93
1.4004-1.42040.21741430.17222708X-RAY DIFFRACTION94
1.4204-1.44160.20381420.16972686X-RAY DIFFRACTION93
1.4416-1.46410.21261290.16742742X-RAY DIFFRACTION94
1.4641-1.48810.23031460.17722695X-RAY DIFFRACTION94
1.4881-1.51380.24451290.19232716X-RAY DIFFRACTION93
1.5138-1.54130.2041260.17682730X-RAY DIFFRACTION94
1.5413-1.57090.21581400.1572734X-RAY DIFFRACTION94
1.5709-1.6030.20951500.15052739X-RAY DIFFRACTION95
1.603-1.63780.18681560.14832699X-RAY DIFFRACTION95
1.6378-1.67590.18971390.14452754X-RAY DIFFRACTION95
1.6759-1.71780.18191580.14332730X-RAY DIFFRACTION95
1.7178-1.76430.2151510.15482761X-RAY DIFFRACTION95
1.7643-1.81620.21191370.15692724X-RAY DIFFRACTION94
1.8162-1.87480.20191420.15462743X-RAY DIFFRACTION95
1.8748-1.94180.18521540.15272720X-RAY DIFFRACTION94
1.9418-2.01950.17171310.13412772X-RAY DIFFRACTION95
2.0195-2.11140.17451430.13832746X-RAY DIFFRACTION95
2.1114-2.22260.20091240.14312758X-RAY DIFFRACTION94
2.2226-2.36180.19061540.15392761X-RAY DIFFRACTION96
2.3618-2.5440.19331300.16482856X-RAY DIFFRACTION98
2.544-2.79980.18321650.15762814X-RAY DIFFRACTION97
2.7998-3.20430.18591450.15742851X-RAY DIFFRACTION98
3.2043-4.03480.14991370.13442926X-RAY DIFFRACTION99
4.0348-26.50640.141260.14162950X-RAY DIFFRACTION98

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