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- PDB-6rem: Crystal structure of Pizza6-SH with Sulphate ion -

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Basic information

Entry
Database: PDB / ID: 6rem
TitleCrystal structure of Pizza6-SH with Sulphate ion
ComponentsPizza6-SH
KeywordsDE NOVO PROTEIN / Artificial beta-propeller protein / computational design / sulphate ion / Pizza
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNoguchi, H. / Clarke, D.E. / Gryspeerdt, J.L. / Feyter, S.D. / Voet, A.R.D.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - FlandersG0E4717N, G0F9316N, G051917N Belgium
CitationJournal: To Be Published
Title: Artificial beta-Propeller Protein-based Hydrolases
Authors: Noguchi, H. / Clarke, D.E. / Gryspeerdt, J.L. / Feyter, S.D. / Voet, A.R.D.
History
DepositionApr 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Pizza6-SH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4497
Polymers25,8731
Non-polymers5766
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-72 kcal/mol
Surface area10260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.007, 56.732, 69.783
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 Pizza6-SH


Mass: 25872.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 1.87 Å3/Da / Density % sol: 34.39 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: 0.2M Ammonium sulfate, 30%(w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→49.01 Å / Num. obs: 26350 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 15.15 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.038 / Net I/σ(I): 17
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1303 / CC1/2: 0.818 / Rpim(I) all: 0.473 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ww9

3ww9


Resolution: 1.6→40.105 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.43
RfactorNum. reflection% reflection
Rfree0.2084 1302 4.95 %
Rwork0.173 --
obs0.1748 26291 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→40.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 30 250 2070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081906
X-RAY DIFFRACTIONf_angle_d0.8852640
X-RAY DIFFRACTIONf_dihedral_angle_d11.851630
X-RAY DIFFRACTIONf_chiral_restr0.291329
X-RAY DIFFRACTIONf_plane_restr0.006347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.66410.25081450.25382728X-RAY DIFFRACTION100
1.6641-1.73980.32031390.22992732X-RAY DIFFRACTION100
1.7398-1.83150.26431410.20992733X-RAY DIFFRACTION100
1.8315-1.94630.24421380.17732747X-RAY DIFFRACTION100
1.9463-2.09650.19891370.16532766X-RAY DIFFRACTION100
2.0965-2.30750.1921650.15752723X-RAY DIFFRACTION100
2.3075-2.64140.18821310.17072807X-RAY DIFFRACTION100
2.6414-3.32760.21921620.17232804X-RAY DIFFRACTION100
3.3276-40.11770.18431440.15832949X-RAY DIFFRACTION100

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