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

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Basic information

Entry
Database: PDB / ID: 3wwf
TitleCrystal structure of the computationally designed Pizza2-SR protein
Componentspizza2sr-pb 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: 1.601 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 / Category: chem_comp_atom / chem_comp_bond / database_2
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: pizza2sr-pb protein
B: pizza2sr-pb protein
C: pizza2sr-pb protein


Theoretical massNumber of molelcules
Total (without water)27,4293
Polymers27,4293
Non-polymers00
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-29 kcal/mol
Surface area10250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.912, 69.701, 103.007
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 pizza2sr-pb protein


Mass: 9143.111 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The protein was designed.
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1M Lithium Chloride, 0.1M Tris-HCl pH 8.0, 20% PEG 6000, 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: 1.6→50 Å / Num. obs: 35121 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 64.88
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 19.32 / % possible all: 99.9

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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: 1.601→28.864 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 22.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2402 1758 5.01 %
Rwork0.1954 --
obs0.1976 35064 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.601→28.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 0 224 1982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061779
X-RAY DIFFRACTIONf_angle_d1.1662442
X-RAY DIFFRACTIONf_dihedral_angle_d9.04612
X-RAY DIFFRACTIONf_chiral_restr0.072315
X-RAY DIFFRACTIONf_plane_restr0.005321
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 (%)
1.6014-1.64460.27121220.22732566100
1.6446-1.6930.25391480.21142552100
1.693-1.74770.23931170.20832613100
1.7477-1.81010.23761290.20452567100
1.8101-1.88260.27311460.19952592100
1.8826-1.96830.2811380.20822586100
1.9683-2.0720.21951550.19462586100
2.072-2.20180.26931450.19512571100
2.2018-2.37170.24991290.19292625100
2.3717-2.61020.23361360.20292629100
2.6102-2.98760.22441320.19692639100
2.9876-3.76280.23551290.1807259396
3.7628-28.86820.22321320.1889218779

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