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- PDB-3ww9: Crystal structure of the computationally designed Pizza6 protein -

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Basic information

Entry
Database: PDB / ID: 3ww9
TitleCrystal structure of the computationally designed Pizza6 protein
Componentspizza6 protein
KeywordsDE NOVO PROTEIN / Computational protein design / Self-assembly
Function / homologyTolB, C-terminal domain / 6 Propeller / Neuraminidase / Mainly Beta
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsVoet, A.R.D. / Noguchi, H. / Addy, C. / Simoncini, D. / Terada, D. / Unzai, S. / Park, S.Y. / Zhang, K.Y.J. / Tame, J.R.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Computational design of a self-assembling symmetrical beta-propeller protein.
Authors: Voet, A.R.D. / Noguchi, H. / Addy, C. / Simoncini, D. / Terada, D. / Unzai, S. / Park, S.Y. / Zhang, K.Y.J. / Tame, J.R.H.
History
DepositionJun 17, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pizza6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5388
Polymers25,8811
Non-polymers6577
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.631, 56.214, 70.101
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein pizza6 protein


Mass: 25881.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The protein was designed.
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 1.85 Å3/Da / Density % sol: 33.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.15M Sodium chloride, 1M Ammonium sulfate, 0.1M HEPES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 13, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→50 Å / Num. obs: 42870 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 9.4 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 64.86
Reflection shellResolution: 1.33→1.35 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 10.99 / % possible all: 65.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_1412)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→39.957 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 17.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1912 2158 5.04 %
Rwork0.1581 --
obs0.1597 42810 95.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.33→39.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 39 246 2075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061851
X-RAY DIFFRACTIONf_angle_d1.1562544
X-RAY DIFFRACTIONf_dihedral_angle_d9.481618
X-RAY DIFFRACTIONf_chiral_restr0.071318
X-RAY DIFFRACTIONf_plane_restr0.006334
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3298-1.36070.20941090.1816190068
1.3607-1.39480.22961040.1686222879
1.3948-1.43250.17991410.1667248689
1.4325-1.47460.19891340.1636271396
1.4746-1.52220.22881470.16092838100
1.5222-1.57670.21541550.15822776100
1.5767-1.63980.19931490.15572798100
1.6398-1.71440.19771390.15832822100
1.7144-1.80480.18931450.1612838100
1.8048-1.91790.19851670.15172805100
1.9179-2.0660.16271420.14522867100
2.066-2.27380.1781410.14662859100
2.2738-2.60280.18821540.16252871100
2.6028-3.2790.21051680.16392891100
3.279-39.97550.17421630.1585296098

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