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- PDB-3ww8: Crystal structure of the computationally designed Pizza3 protein -

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Basic information

Entry
Database: PDB / ID: 3ww8
TitleCrystal structure of the computationally designed Pizza3 protein
ComponentsPizza3 protein
KeywordsDE NOVO PROTEIN / Computational protein design / Self-assembly
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.402 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

Downloads & links

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Assembly

Deposited unit
A: Pizza3 protein
B: Pizza3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6936
Polymers26,3132
Non-polymers3804
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-56 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.882, 56.213, 69.966
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 Pizza3 protein


Mass: 13156.454 Da / Num. of mol.: 2 / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 1.83 Å3/Da / Density % sol: 32.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.6M Ammonium sulfate, 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: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 28, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 37433 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 40.16
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 3.88 / % possible all: 95.1

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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: 1.402→40.071 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2232 1855 4.97 %
Rwork0.1856 --
obs0.1875 37358 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.402→40.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 21 217 2024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061831
X-RAY DIFFRACTIONf_angle_d1.1582521
X-RAY DIFFRACTIONf_dihedral_angle_d8.671610
X-RAY DIFFRACTIONf_chiral_restr0.077318
X-RAY DIFFRACTIONf_plane_restr0.006332
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4023-1.44020.27611270.2698257993
1.4402-1.48260.31241150.2452276699
1.4826-1.53040.27771390.22552744100
1.5304-1.58510.25991510.20092779100
1.5851-1.64860.25481540.19952762100
1.6486-1.72360.26281690.18692769100
1.7236-1.81450.26371300.19312815100
1.8145-1.92820.21741600.16932755100
1.9282-2.07710.21341410.16812825100
2.0771-2.28610.19381370.16062809100
2.2861-2.61680.18881270.179284799
2.6168-3.29670.20971730.1764274896
3.2967-40.08740.22141320.1945230577

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