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- PDB-6reo: Crystal structure of 3fPizza6-SH with Sulphate ion -

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Basic information

Entry
Database: PDB / ID: 6reo
TitleCrystal structure of 3fPizza6-SH with Sulphate ion
Components3fPizza6-SH
KeywordsDE NOVO PROTEIN / Artificial beta-propeller protein / computational design / Pizza / Sulphate
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.0Nov 18, 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: 3fPizza6-SH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,02513
Polymers25,8731
Non-polymers1,15312
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-130 kcal/mol
Surface area10500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.953, 57.580, 69.690
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 3fPizza6-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.: 12 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 1.9 Å3/Da / Density % sol: 35.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: 0.2M Ammonium bromide, 2.2M Ammonium sulphate

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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: Jul 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→26.61 Å / Num. obs: 32268 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 14.52 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.042 / Net I/σ(I): 13
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1585 / CC1/2: 0.686 / Rpim(I) all: 0.535 / % possible all: 100

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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: 1.5→26.609 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.79
RfactorNum. reflection% reflection
Rfree0.2044 1671 5.19 %
Rwork0.1669 --
obs0.1688 32211 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→26.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 60 263 2113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041951
X-RAY DIFFRACTIONf_angle_d0.7042712
X-RAY DIFFRACTIONf_dihedral_angle_d9.741638
X-RAY DIFFRACTIONf_chiral_restr0.058338
X-RAY DIFFRACTIONf_plane_restr0.005352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.54420.30151330.24562516X-RAY DIFFRACTION100
1.5442-1.5940.26061280.22162500X-RAY DIFFRACTION100
1.594-1.65090.2521470.22012502X-RAY DIFFRACTION100
1.6509-1.7170.20841250.19762520X-RAY DIFFRACTION100
1.717-1.79520.20151390.19342519X-RAY DIFFRACTION100
1.7952-1.88980.23541340.17422547X-RAY DIFFRACTION100
1.8898-2.00820.18881530.16912491X-RAY DIFFRACTION100
2.0082-2.16310.18831270.16232543X-RAY DIFFRACTION100
2.1631-2.38070.20081430.15832541X-RAY DIFFRACTION100
2.3807-2.72490.22231670.17122546X-RAY DIFFRACTION100
2.7249-3.43190.19181240.15742611X-RAY DIFFRACTION100
3.4319-26.6130.18721510.14792704X-RAY DIFFRACTION100

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