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- PDB-6y25: Streptavidin mutant S112R,K121E with a biotC4-1 cofactor - an art... -

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Basic information

Entry
Database: PDB / ID: 6y25
TitleStreptavidin mutant S112R,K121E with a biotC4-1 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
biotC4-1 cofactor / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 14, 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)17,3072
Polymers16,6391
Non-polymers6681
Water1,18966
1
AAA: Streptavidin
hetero molecules

AAA: Streptavidin
hetero molecules

AAA: Streptavidin
hetero molecules

AAA: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2278
Polymers66,5564
Non-polymers2,6704
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 area10010 Å2
ΔGint-53 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.146, 57.146, 182.564
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-316-

HOH

21AAA-343-

HOH

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Components

#1: Protein Streptavidin


Mass: 16639.082 Da / Num. of mol.: 1 / Mutation: S112R, K121E
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-O6T / biotC4-1 cofactor


Mass: 667.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H37FeN7O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.08 %
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: 1.95→45.683 Å / Num. obs: 11549 / % possible obs: 100 % / Redundancy: 23.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Net I/σ(I): 23.2
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 1.9 / Num. unique obs: 561 / CC1/2: 0.907

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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: 1.95→45.683 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.195 / WRfactor Rwork: 0.184 / Average fsc free: 0.9379 / Average fsc work: 0.9382 / Cross valid method: FREE R-VALUE / ESU R: 0.151 / ESU R Free: 0.125
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2035 576 5.022 %
Rwork0.1938 10893 -
all0.194 --
obs-11469 99.419 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.601 Å2
Baniso -1Baniso -2Baniso -3
1-0.405 Å20 Å20 Å2
2--0.405 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms909 0 44 66 1019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013999
X-RAY DIFFRACTIONr_bond_other_d0.0390.018799
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.731387
X-RAY DIFFRACTIONr_angle_other_deg2.5461.5721842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1045124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.69522.548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57915126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.156155
X-RAY DIFFRACTIONr_chiral_restr0.0780.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021136
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02222
X-RAY DIFFRACTIONr_nbd_refined0.220.2174
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2280.2715
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2482
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2413
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.250
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2540.225
X-RAY DIFFRACTIONr_nbd_other0.230.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2140.210
X-RAY DIFFRACTIONr_mcbond_it3.2883.782493
X-RAY DIFFRACTIONr_mcbond_other3.2743.779492
X-RAY DIFFRACTIONr_mcangle_it4.1735.663618
X-RAY DIFFRACTIONr_mcangle_other4.1755.667619
X-RAY DIFFRACTIONr_scbond_it4.034.068505
X-RAY DIFFRACTIONr_scbond_other4.0564.052456
X-RAY DIFFRACTIONr_scangle_it5.5715.996767
X-RAY DIFFRACTIONr_scangle_other5.6385.933684
X-RAY DIFFRACTIONr_lrange_it7.21144.3781132
X-RAY DIFFRACTIONr_lrange_other7.19843.1341070
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.261510.267781X-RAY DIFFRACTION99.1657
2.001-2.0550.265370.286752X-RAY DIFFRACTION98.5019
2.055-2.1150.331470.287732X-RAY DIFFRACTION98.9835
2.115-2.180.202420.231730X-RAY DIFFRACTION100
2.18-2.2510.206210.261709X-RAY DIFFRACTION98.916
2.251-2.330.232410.235673X-RAY DIFFRACTION99.1667
2.33-2.4180.198400.193659X-RAY DIFFRACTION100
2.418-2.5170.227330.193644X-RAY DIFFRACTION100
2.517-2.6290.186340.216615X-RAY DIFFRACTION100
2.629-2.7570.197350.196580X-RAY DIFFRACTION99.6758
2.757-2.9060.187290.191571X-RAY DIFFRACTION99.8336
2.906-3.0820.2210.162535X-RAY DIFFRACTION99.8205
3.082-3.2950.158220.177513X-RAY DIFFRACTION99.8134
3.295-3.5580.21330.185468X-RAY DIFFRACTION99.6024
3.558-3.8970.167200.166437X-RAY DIFFRACTION97.8587
3.897-4.3560.218180.161402X-RAY DIFFRACTION99.0566
4.356-5.0280.154200.151361X-RAY DIFFRACTION100
5.028-6.1540.219140.174314X-RAY DIFFRACTION100
6.154-8.6830.093110.202254X-RAY DIFFRACTION100
8.683-45.6830.32170.254163X-RAY DIFFRACTION99.4152

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