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- PDB-6y34: Streptavidin wildtype with a biotC5-1 cofactor - an artificial ir... -

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Basic information

Entry
Database: PDB / ID: 6y34
TitleStreptavidin wildtype 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: 1.307 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)17,3433
Polymers16,5691
Non-polymers7742
Water2,378132
1
AAA: Streptavidin
hetero molecules

AAA: Streptavidin
hetero molecules

AAA: Streptavidin
hetero molecules

AAA: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,37112
Polymers66,2764
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 area9110 Å2
ΔGint-53 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.941, 57.941, 183.822
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-304-

HOH

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Components

#1: Protein Streptavidin


Mass: 16569.031 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.: 132 / 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: 2.33 Å3/Da / Density % sol: 47.16 %
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: 1.307→45.998 Å / Num. obs: 38242 / % possible obs: 99.3 % / Redundancy: 25.4 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Net I/σ(I): 26.2
Reflection shellResolution: 1.307→1.33 Å / Redundancy: 22.9 % / Rmerge(I) obs: 2.702 / Num. unique obs: 1785 / CC1/2: 0.552 / % possible all: 95.4

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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: 1.307→45.998 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.198 / WRfactor Rwork: 0.178 / Average fsc free: 0.912 / Average fsc work: 0.9175 / Cross valid method: FREE R-VALUE / ESU R: 0.044 / ESU R Free: 0.046
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1978 1873 4.917 %
Rwork0.1797 36218 -
all0.181 --
obs-38091 98.915 %
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: 18.282 Å2
Baniso -1Baniso -2Baniso -3
1-0.179 Å20 Å20 Å2
2--0.179 Å20 Å2
3----0.359 Å2
Refinement stepCycle: LAST / Resolution: 1.307→45.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms904 0 23 132 1059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.013976
X-RAY DIFFRACTIONr_bond_other_d0.0380.018817
X-RAY DIFFRACTIONr_angle_refined_deg2.2351.6691339
X-RAY DIFFRACTIONr_angle_other_deg2.691.5721887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1365126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.13422.72744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09315128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.243154
X-RAY DIFFRACTIONr_chiral_restr0.3090.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021127
X-RAY DIFFRACTIONr_gen_planes_other0.020.02219
X-RAY DIFFRACTIONr_nbd_refined0.1940.2141
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2320.2709
X-RAY DIFFRACTIONr_nbtor_refined0.180.2463
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2470
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.271
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1770.28
X-RAY DIFFRACTIONr_nbd_other0.1980.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0760.210
X-RAY DIFFRACTIONr_mcbond_it1.8071.752498
X-RAY DIFFRACTIONr_mcbond_other1.7771.748497
X-RAY DIFFRACTIONr_mcangle_it2.6372.623626
X-RAY DIFFRACTIONr_mcangle_other2.6362.627627
X-RAY DIFFRACTIONr_scbond_it2.9931.975478
X-RAY DIFFRACTIONr_scbond_other2.991.979479
X-RAY DIFFRACTIONr_scangle_it4.5052.848712
X-RAY DIFFRACTIONr_scangle_other4.5022.851713
X-RAY DIFFRACTIONr_lrange_it6.02721.3511087
X-RAY DIFFRACTIONr_lrange_other5.81720.4991051
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.307-1.3410.491230.4212577X-RAY DIFFRACTION96.532
1.341-1.3770.2981370.3332527X-RAY DIFFRACTION97.2263
1.377-1.4170.3571380.2992501X-RAY DIFFRACTION100
1.417-1.4610.3071100.2462481X-RAY DIFFRACTION100
1.461-1.5090.2751190.2352376X-RAY DIFFRACTION99.9199
1.509-1.5620.2041220.1832322X-RAY DIFFRACTION100
1.562-1.6210.1831300.1732194X-RAY DIFFRACTION100
1.621-1.6870.1861200.1572140X-RAY DIFFRACTION100
1.687-1.7620.1961210.1652046X-RAY DIFFRACTION99.678
1.762-1.8480.192990.1631909X-RAY DIFFRACTION96.2608
1.848-1.9480.211820.1961836X-RAY DIFFRACTION96.9176
1.948-2.0660.19810.1791807X-RAY DIFFRACTION99.9471
2.066-2.2080.174880.1691682X-RAY DIFFRACTION100
2.208-2.3850.189690.1711537X-RAY DIFFRACTION96.9807
2.385-2.6130.177840.1531455X-RAY DIFFRACTION99.8702
2.613-2.9210.219640.1611348X-RAY DIFFRACTION100
2.921-3.3720.159750.1621145X-RAY DIFFRACTION98.0707
3.372-4.1290.145440.1511028X-RAY DIFFRACTION99.5357
4.129-5.8330.169390.168817X-RAY DIFFRACTION100
5.833-45.9980.297280.232490X-RAY DIFFRACTION99.6154

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