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

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Basic information

Entry
Database: PDB / ID: 3wwb
TitleCrystal structure of the computationally designed Pizza2-SR protein
ComponentsPizza2-SR 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: 1.7 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

Downloads & links

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Assembly

Deposited unit
A: Pizza2-SR protein
B: Pizza2-SR protein
C: Pizza2-SR protein


Theoretical massNumber of molelcules
Total (without water)27,4293
Polymers27,4293
Non-polymers00
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-29 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.449, 63.695, 69.903
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-SR 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.: 239 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
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: 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: 1.7→50 Å / Num. obs: 30689 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 44.59
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 7.28 / % possible all: 100

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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: 1.7→34.952 Å / SU ML: 0.16 / σ(F): 1.33 / Phase error: 18.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2022 1544 5.04 %
Rwork0.1704 --
obs0.1721 30629 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→34.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 0 239 2003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071790
X-RAY DIFFRACTIONf_angle_d1.182459
X-RAY DIFFRACTIONf_dihedral_angle_d8.833617
X-RAY DIFFRACTIONf_chiral_restr0.076318
X-RAY DIFFRACTIONf_plane_restr0.005323
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7002-1.75510.24321450.2027259699
1.7551-1.81780.23781540.19972603100
1.8178-1.89060.22191440.18062609100
1.8906-1.97660.18711390.16592625100
1.9766-2.08080.21871410.16182620100
2.0808-2.21120.2081250.17242679100
2.2112-2.38180.20311370.16492640100
2.3818-2.62150.20331430.18672652100
2.6215-3.00060.21141350.17912685100
3.0006-3.77970.1921300.16252705100
3.7797-34.95890.18451510.1578267194

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