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- PDB-6fh8: E. coli surface display of streptavidin for directed evolution of... -

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Basic information

Entry
Database: PDB / ID: 6fh8
TitleE. coli surface display of streptavidin for directed evolution of an allylic deallocase
ComponentsStreptavidin
Keywordsbiotin binding protein / artificial metalloenzyme / E. coli surface display / streptavidin / biotin / bioorthogonal reaction / uncaging / allyl deprotection / directed evolution
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin ...Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
biotinylated ruthenium cyclopentadienide / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.64 Å
AuthorsHeinisch, T. / Schwizer, F. / Garabedian, B. / Csibra, E. / Jeschek, M. / Pinheiro Bernhardes, V. / Marliere, P. / Panke, S. / Ward, T.R.
CitationJournal: Chem Sci / Year: 2018
Title: E. colisurface display of streptavidin for directed evolution of an allylic deallylase.
Authors: Heinisch, T. / Schwizer, F. / Garabedian, B. / Csibra, E. / Jeschek, M. / Vallapurackal, J. / Pinheiro, V.B. / Marliere, P. / Panke, S. / Ward, T.R.
History
DepositionJan 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2162
Polymers16,5561
Non-polymers6601
Water1,42379
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8638
Polymers66,2244
Non-polymers2,6394
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_555y,x,-z1
Buried area9430 Å2
ΔGint-58 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.722, 57.722, 183.615
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

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Components

#1: Protein Streptavidin


Mass: 16556.033 Da / Num. of mol.: 1 / Mutation: S112M-K121A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Chemical ChemComp-JCT / biotinylated ruthenium cyclopentadienide


Mass: 659.698 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H28N5O5RuS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 2.0 M ammonium sulfate, 0.1 M sodium acetate, pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→45.8 Å / Num. obs: 19391 / % possible obs: 98.3 % / Redundancy: 15.7 % / Net I/σ(I): 26.9
Reflection shellResolution: 1.64→1.66 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementResolution: 1.64→45.8 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.609 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.064 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15905 952 4.9 %RANDOM
Rwork0.12016 ---
obs0.12208 18415 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.139 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2---0.33 Å20 Å2
3---0.65 Å2
Refinement stepCycle: 1 / Resolution: 1.64→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms934 0 41 79 1054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.021002
X-RAY DIFFRACTIONr_bond_other_d0.0020.02830
X-RAY DIFFRACTIONr_angle_refined_deg2.3121.9351372
X-RAY DIFFRACTIONr_angle_other_deg1.19231911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9455126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.98523.65941
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44415133
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.073155
X-RAY DIFFRACTIONr_chiral_restr0.1440.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021144
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02218
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9862.274501
X-RAY DIFFRACTIONr_mcbond_other3.962.264500
X-RAY DIFFRACTIONr_mcangle_it4.653.403625
X-RAY DIFFRACTIONr_mcangle_other4.6463.412626
X-RAY DIFFRACTIONr_scbond_it7.0062.776500
X-RAY DIFFRACTIONr_scbond_other5.7832.701461
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9933.835690
X-RAY DIFFRACTIONr_long_range_B_refined10.10627.8351135
X-RAY DIFFRACTIONr_long_range_B_other5.98327.0691064
X-RAY DIFFRACTIONr_rigid_bond_restr6.06731829
X-RAY DIFFRACTIONr_sphericity_free28.615562
X-RAY DIFFRACTIONr_sphericity_bonded15.08851821
LS refinement shellResolution: 1.636→1.678 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 54 -
Rwork0.252 1116 -
obs--82.57 %

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