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- PDB-3ww7: Crystal structure of the computationally designed Pizza2 protein -

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Basic information

Entry
Database: PDB / ID: 3ww7
TitleCrystal structure of the computationally designed Pizza2 protein
ComponentsPizza2 protein
KeywordsDE NOVO PROTEIN / Computational protein design / Self-assembly
Function / homologyThrombin, subunit H - #500 / Thrombin, subunit H / Beta Barrel / Mainly Beta
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.697 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: Pizza2 protein
B: Pizza2 protein
C: Pizza2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0216
Polymers26,7443
Non-polymers2763
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-30 kcal/mol
Surface area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.235, 69.709, 91.104
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 Pizza2 protein


Mass: 8914.796 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The protein was designed.
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20mM Magnesium chloride, 100mM HEPES pH 7.5, 22% Polyacrylic acid 5100 Sodium sult, 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
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 wavelengthRelative weight: 1
ReflectionResolution: 1.697→50 Å / Num. obs: 27597 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 29.93
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 5.09 / % possible all: 91.1

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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: 1.697→35.491 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 21.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 1405 5.1 %
Rwork0.1741 --
obs0.1765 27568 92.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.697→35.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 18 240 2022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061806
X-RAY DIFFRACTIONf_angle_d1.1312481
X-RAY DIFFRACTIONf_dihedral_angle_d8.557606
X-RAY DIFFRACTIONf_chiral_restr0.071315
X-RAY DIFFRACTIONf_plane_restr0.006327
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6973-1.7580.27441340.2323248889
1.758-1.82840.25531440.2185254892
1.8284-1.91160.26051420.1964255292
1.9116-2.01240.24731240.1841258692
2.0124-2.13840.22131530.1738255792
2.1384-2.30350.25151230.1684256391
2.3035-2.53530.23541420.184262093
2.5353-2.9020.24291410.1788273496
2.902-3.65560.1971640.1587275697
3.6556-35.49840.18061380.1538275992

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