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- PDB-6y2t: Streptavidin wildtype with a biotC4-1 cofactor - an artificial ir... -

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Basic information

Entry
Database: PDB / ID: 6y2t
TitleStreptavidin wildtype 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: 1.55 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)18,0885
Polymers16,5691
Non-polymers1,5194
Water1,820101
1
AAA: Streptavidin
hetero molecules

AAA: Streptavidin
hetero molecules

AAA: Streptavidin
hetero molecules

AAA: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,35320
Polymers66,2764
Non-polymers6,07716
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 area12660 Å2
ΔGint-55 kcal/mol
Surface area17880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.714, 57.714, 184.135
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-327-

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-O6T / biotC4-1 cofactor


Mass: 667.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H37FeN7O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 3 Å3/Da / Density % sol: 58.99 %
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: 1.55→46.076 Å / Num. obs: 23212 / % possible obs: 100 % / Redundancy: 25.3 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Net I/σ(I): 28.8
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 1.704 / Num. unique obs: 1135 / CC1/2: 0.793 / % possible all: 100

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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: 1.55→46.076 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.072
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2004 1161 5.009 %
Rwork0.1688 --
all0.17 --
obs-23178 99.931 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.969 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.55→46.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms904 0 100 101 1105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131065
X-RAY DIFFRACTIONr_bond_other_d0.0380.018827
X-RAY DIFFRACTIONr_angle_refined_deg2.1651.8011493
X-RAY DIFFRACTIONr_angle_other_deg2.5141.5721909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3675128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.22622.72744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.95415128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.562154
X-RAY DIFFRACTIONr_chiral_restr0.0840.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021158
X-RAY DIFFRACTIONr_gen_planes_other0.0230.02220
X-RAY DIFFRACTIONr_nbd_refined0.2080.2160
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2310.2725
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2486
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2441
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.253
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.380.225
X-RAY DIFFRACTIONr_nbd_other0.2390.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0990.217
X-RAY DIFFRACTIONr_mcbond_it2.2912.305500
X-RAY DIFFRACTIONr_mcbond_other2.1882.302499
X-RAY DIFFRACTIONr_mcangle_it3.2483.448629
X-RAY DIFFRACTIONr_mcangle_other3.2543.452630
X-RAY DIFFRACTIONr_scbond_it3.3082.725563
X-RAY DIFFRACTIONr_scbond_other3.3052.729564
X-RAY DIFFRACTIONr_scangle_it4.7643.993859
X-RAY DIFFRACTIONr_scangle_other4.7613.999860
X-RAY DIFFRACTIONr_lrange_it6.55828.7541145
X-RAY DIFFRACTIONr_lrange_other6.53128.4541133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.228840.2281586X-RAY DIFFRACTION100
1.59-1.6340.231830.2121571X-RAY DIFFRACTION100
1.634-1.6810.215790.1891498X-RAY DIFFRACTION100
1.681-1.7330.239770.2031477X-RAY DIFFRACTION100
1.733-1.790.215760.1651433X-RAY DIFFRACTION99.9338
1.79-1.8520.163730.1511383X-RAY DIFFRACTION100
1.852-1.9220.169700.1621337X-RAY DIFFRACTION99.5754
1.922-2.0010.166670.1591283X-RAY DIFFRACTION99.926
2.001-2.090.228660.1651250X-RAY DIFFRACTION100
2.09-2.1920.197630.1541190X-RAY DIFFRACTION100
2.192-2.310.175600.1561146X-RAY DIFFRACTION100
2.31-2.450.205560.151061X-RAY DIFFRACTION100
2.45-2.6190.157540.1451024X-RAY DIFFRACTION100
2.619-2.8290.192500.162947X-RAY DIFFRACTION100
2.829-3.0990.222470.156882X-RAY DIFFRACTION100
3.099-3.4640.193420.167802X-RAY DIFFRACTION99.8817
3.464-3.9990.157380.15719X-RAY DIFFRACTION100
3.999-4.8950.169330.136623X-RAY DIFFRACTION100
4.895-6.9130.227260.203497X-RAY DIFFRACTION100
6.913-46.0760.338170.314308X-RAY DIFFRACTION99.6933

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