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- PDB-3wwa: Crystal structure of the computationally designed Pizza7 protein ... -

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Basic information

Entry
Database: PDB / ID: 3wwa
TitleCrystal structure of the computationally designed Pizza7 protein after heat treatment
ComponentsPizza7H protein
KeywordsDE NOVO PROTEIN / Computational protein design / Self-assembly
Function / homologyTolB, C-terminal domain / 6 Propeller / Neuraminidase / Mainly Beta / ISOPROPYL ALCOHOL
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.988 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: Pizza7H protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1832
Polymers30,1231
Non-polymers601
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.056, 69.498, 92.301
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 Pizza7H protein


Mass: 30123.080 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The protein was designed.
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.085M HEPES Sodium Salt pH 7.5, 8.5% Isopropanol, 17% PEG 4000, 15% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 19, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.988→50 Å / Num. obs: 17958 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 39.27
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 8.69 / % possible all: 99.8

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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: 1.988→34.704 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2585 910 5.08 %
Rwork0.1932 --
obs0.1966 17919 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.988→34.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 4 93 1887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071822
X-RAY DIFFRACTIONf_angle_d1.2232509
X-RAY DIFFRACTIONf_dihedral_angle_d8.758610
X-RAY DIFFRACTIONf_chiral_restr0.084318
X-RAY DIFFRACTIONf_plane_restr0.005334
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9881-2.11270.30111350.2332275796
2.1127-2.27580.28041620.22622803100
2.2758-2.50470.31621490.22222905100
2.5047-2.8670.2791330.2182896100
2.867-3.61150.25611520.1817288199
3.6115-34.70960.22661790.1648276792

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