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- PDB-6gmi: Genetic Engineering of an Artificial Metalloenzyme for Transfer H... -

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Basic information

Entry
Database: PDB / ID: 6gmi
TitleGenetic Engineering of an Artificial Metalloenzyme for Transfer Hydrogenation of a Self-Immolative Substrate in E. coli's Periplasm.
ComponentsStreptavidin
Keywordsbiotin-binding protein / Artificial Transfer Hydrogenase / Beta Barrel / Streptavidin
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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-4IR / IRIDIUM (III) ION / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRebelein, J.G.
Funding support Switzerland, Germany, 4items
OrganizationGrant numberCountry
Swiss National Science Foundation200020_162348 Switzerland
European Research CouncilDrEAM
Swiss National Science FoundationNCCR MSE Switzerland
European Molecular Biology OrganizationALTF 194-2017 Germany
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Genetic Engineering of an Artificial Metalloenzyme for Transfer Hydrogenation of a Self-Immolative Substrate in Escherichia coli's Periplasm.
Authors: Zhao, J. / Rebelein, J.G. / Mallin, H. / Trindler, C. / Pellizzoni, M.M. / Ward, T.R.
History
DepositionMay 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2016
Polymers18,6241
Non-polymers1,5765
Water61334
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,80224
Polymers74,4974
Non-polymers6,30520
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 area11680 Å2
ΔGint-161 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.507, 57.507, 184.130
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-302-

HOH

21A-307-

HOH

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Components

#1: Protein Streptavidin


Mass: 18624.266 Da / Num. of mol.: 1 / Mutation: S112V, E116SPLSEALTKANSPAEAYKASRGAGA, K121A
Source method: isolated from a genetically manipulated source
Details: T7-Tag on the N-Terminus of Streptavidin, Insertion of SPLSEALTKANSPAEAYKASRGAGA for E116
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Chemical ChemComp-4IR / {N-(4-{[2-(amino-kappaN)ethyl]sulfamoyl-kappaN}phenyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide}(chloro)[(1,2,3,4,5-eta)-1,2,3,4,5-pentamethylcyclopentadienyl]iridium(III) / N-(4-{[(2-AMINOETHYL)AMINO]SULFONYL}PHENYL)-5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANAMIDE-(1,2,3,4,5,6-ETA)-PENTAMETHYLCYCLOHEXYL-CHLORO-IRIDIUM(III)


Mass: 807.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H45ClIrN5O4S2
#3: Chemical
ChemComp-IR3 / IRIDIUM (III) ION


Mass: 192.217 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ir
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.04 Å3/Da / Density % sol: 39.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M SPG 9 pH (Buffer) 25 %w/v PEG 1500 (Precipitant)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→46.07 Å / Num. obs: 20991 / % possible obs: 100 % / Redundancy: 25.4 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 15.6
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 4.33

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2qcb

2qcb


Resolution: 1.6→46.07 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.7 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.073 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 1065 5.1 %RANDOM
Rwork0.18661 ---
obs0.18728 19899 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.467 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.37 Å20 Å2
3---0.75 Å2
Refinement stepCycle: 1 / Resolution: 1.6→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms896 0 45 34 975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.014988
X-RAY DIFFRACTIONr_bond_other_d0.0010.018790
X-RAY DIFFRACTIONr_angle_refined_deg2.5231.7531395
X-RAY DIFFRACTIONr_angle_other_deg1.041.6481833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1455124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.83622.55843
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88715125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.461154
X-RAY DIFFRACTIONr_chiral_restr0.0850.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021126
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02200
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_it3.0122.968490
X-RAY DIFFRACTIONr_mcbond_other2.9262.962489
X-RAY DIFFRACTIONr_mcangle_it4.0624.415613
X-RAY DIFFRACTIONr_mcangle_other4.0594.421614
X-RAY DIFFRACTIONr_scbond_it3.5743.239498
X-RAY DIFFRACTIONr_scbond_other3.5333.202450
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.264.654678
X-RAY DIFFRACTIONr_long_range_B_refined8.22734.6071082
X-RAY DIFFRACTIONr_long_range_B_other8.22734.3491034
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 82 -
Rwork0.292 1425 -
obs--100 %

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