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- PDB-6y33: Streptavidin mutant S112R with a biotC5-1 cofactor - an artificia... -

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Basic information

Entry
Database: PDB / ID: 6y33
TitleStreptavidin mutant S112R with a biotC5-1 cofactor - an artificial iron hydroxylase
ComponentsStreptavidin
KeywordsOXIDOREDUCTASE / Artificial Metalloenzyme / Iron Hydroxylase / Biotin-Binding Protein
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile.
Similarity search - Domain/homology
biotC5-1 cofactor / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsSerrano-Plana, J. / Rumo, C. / Rebelein, J.G. / Peterson, R.L. / Barnet, M. / Ward, T.R.
Funding support Switzerland, European Union, Germany, 5items
OrganizationGrant numberCountry
Swiss National Science Foundation200020_182046 Switzerland
Swiss National Science FoundationNCCR MSE Switzerland
European Research Council (ERC)694424European Union
European Molecular Biology Organization (EMBO)ALTF 194-2017 Germany
European Research Council (ERC)H2020-MSCA-IF-2016European Union
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Enantioselective Hydroxylation of Benzylic C(sp3)-H Bonds by an Artificial Iron Hydroxylase Based on the Biotin-Streptavidin Technology.
Authors: Serrano-Plana, J. / Rumo, C. / Rebelein, J.G. / Peterson, R.L. / Barnet, M. / Ward, T.R.
History
DepositionFeb 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4133
Polymers16,6391
Non-polymers7742
Water1,40578
1
AAA: Streptavidin
hetero molecules

AAA: Streptavidin
hetero molecules

AAA: Streptavidin
hetero molecules

AAA: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,65112
Polymers66,5574
Non-polymers3,0958
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area10360 Å2
ΔGint-61 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.633, 57.633, 183.649
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11AAA-305-

HOH

21AAA-325-

HOH

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Components

#1: Protein Streptavidin


Mass: 16639.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P22629
#2: Chemical ChemComp-O7Q / biotC5-1 cofactor


Mass: 681.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H39FeN7O6S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 2 M (NH4)2SO4, 0.1 M Na-Acetate, pH 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→45.91 Å / Num. obs: 25967 / % possible obs: 99.6 % / Redundancy: 24.9 % / CC1/2: 1 / Rmerge(I) obs: 0.094 / Net I/σ(I): 19.3
Reflection shellResolution: 1.49→1.51 Å / Redundancy: 23 % / Rmerge(I) obs: 2.7 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1160 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PK2

3pk2


Resolution: 1.49→45.91 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / Cross valid method: FREE R-VALUE / ESU R: 0.058 / ESU R Free: 0.06
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1916 1284 4.95 %
Rwork0.1688 --
all0.17 --
obs-25938 99.524 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.078 Å20 Å20 Å2
2--0.078 Å20 Å2
3----0.155 Å2
Refinement stepCycle: LAST / Resolution: 1.49→45.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 23 78 1025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.013993
X-RAY DIFFRACTIONr_bond_other_d0.0380.018837
X-RAY DIFFRACTIONr_angle_refined_deg1.9791.6691359
X-RAY DIFFRACTIONr_angle_other_deg2.5271.5751928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.315128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.41421.66748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.71415132
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.269156
X-RAY DIFFRACTIONr_chiral_restr0.0890.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021153
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02231
X-RAY DIFFRACTIONr_nbd_refined0.1740.2149
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2230.2757
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2466
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2442
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.239
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1670.211
X-RAY DIFFRACTIONr_nbd_other0.2160.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1210.29
X-RAY DIFFRACTIONr_mcbond_it2.1562.162506
X-RAY DIFFRACTIONr_mcbond_other2.0952.157505
X-RAY DIFFRACTIONr_mcangle_it3.2333.232636
X-RAY DIFFRACTIONr_mcangle_other3.2353.235637
X-RAY DIFFRACTIONr_scbond_it3.2762.417486
X-RAY DIFFRACTIONr_scbond_other3.2722.419487
X-RAY DIFFRACTIONr_scangle_it4.8443.488722
X-RAY DIFFRACTIONr_scangle_other4.843.493723
X-RAY DIFFRACTIONr_lrange_it6.02924.841079
X-RAY DIFFRACTIONr_lrange_other6.01324.6831073
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.5250.344890.2941690X-RAY DIFFRACTION94.88
1.525-1.5670.222840.2371765X-RAY DIFFRACTION100
1.567-1.6120.301780.2251702X-RAY DIFFRACTION100
1.612-1.6620.203930.1951657X-RAY DIFFRACTION100
1.662-1.7170.242760.1751618X-RAY DIFFRACTION100
1.717-1.7770.176800.1531559X-RAY DIFFRACTION100
1.777-1.8440.17920.1441487X-RAY DIFFRACTION99.4959
1.844-1.9190.163910.151431X-RAY DIFFRACTION100
1.919-2.0040.16810.1531387X-RAY DIFFRACTION100
2.004-2.1020.218580.1541350X-RAY DIFFRACTION100
2.102-2.2160.187740.1481280X-RAY DIFFRACTION100
2.216-2.350.182540.1521211X-RAY DIFFRACTION100
2.35-2.5120.167650.151151X-RAY DIFFRACTION100
2.512-2.7130.196590.1741063X-RAY DIFFRACTION100
2.713-2.9720.17510.158988X-RAY DIFFRACTION100
2.972-3.3220.172360.146909X-RAY DIFFRACTION99.1605
3.322-3.8360.205490.159807X-RAY DIFFRACTION99.8833
3.836-4.6960.207290.15693X-RAY DIFFRACTION100
4.696-6.6320.188270.206561X-RAY DIFFRACTION100
6.632-45.910.208180.278345X-RAY DIFFRACTION99.7253

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