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- PDB-8by0: streptavidin mutant S112I K121R with an iridium catalyst for CH a... -

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Basic information

Entry
Database: PDB / ID: 8by0
Titlestreptavidin mutant S112I K121R with an iridium catalyst for CH activation
ComponentsStreptavidin
KeywordsUNKNOWN FUNCTION / Artificial Metalloenzyme
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
Chem-NOF / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsIgareta, N.V. / Ward, T.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: streptavidin mutant S112I with an iridium catalyst for CH activation
Authors: Igareta, N.V. / Ward, T.R.
History
DepositionDec 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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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)17,5334
Polymers16,4931
Non-polymers1,0403
Water21612
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,13016
Polymers65,9724
Non-polymers4,15812
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 area10760 Å2
ΔGint-112 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.428, 57.428, 183.123
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
11A-203-

SO4

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Components

#1: Protein Streptavidin


Mass: 16492.914 Da / Num. of mol.: 1
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-NOF / tert-butyl 7'-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]-1-chloranyl-2,3,4,5,6-pentamethyl-spiro[1$l^{8}-iridapentacyclo[2.2.0.0^{1,3}.0^{1,5}.0^{2,6}]hexane-1,2'-3-aza-1-azonia-2$l^{8}-iridatricyclo[6.3.1.0^{4,12}]dodeca-1(11),4,6,8(12),9-pentaene]-3'-carboxylate / iridium catalyst for CH activation


Mass: 847.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H45ClIrN5O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 2.0 M ammonium sulfate 0.1 M sodium acetate (soaking under pH 6.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99988 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 2.1→45.78 Å / Num. obs: 9422 / % possible obs: 99.8 % / Redundancy: 15.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.065 / Rrim(I) all: 0.191 / Net I/σ(I): 10.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.91-45.7812.10.0471630.9980.0170.05
2.1-2.1616.52.2797550.5730.8242.424

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→41.862 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.258 / SU ML: 0.189 / Cross valid method: NONE / ESU R: 0.211 / ESU R Free: 0.182
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2507 449 4.877 %
Rwork0.2143 8757 -
all0.216 --
obs-9206 97.718 %
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: 44.64 Å2
Baniso -1Baniso -2Baniso -3
1--2.85 Å20 Å2-0 Å2
2---2.85 Å2-0 Å2
3---5.7 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 0 56 12 996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121015
X-RAY DIFFRACTIONr_bond_other_d0.0010.016845
X-RAY DIFFRACTIONr_angle_refined_deg2.1741.7471420
X-RAY DIFFRACTIONr_angle_other_deg0.9211.621944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.195122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.99157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27110129
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.5171044
X-RAY DIFFRACTIONr_chiral_restr0.0690.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02216
X-RAY DIFFRACTIONr_nbd_refined0.2190.2161
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.2803
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2480
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1040.2519
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.224
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1540.224
X-RAY DIFFRACTIONr_nbd_other0.1330.2102
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0550.26
X-RAY DIFFRACTIONr_mcbond_it3.344.458489
X-RAY DIFFRACTIONr_mcbond_other3.3384.464490
X-RAY DIFFRACTIONr_mcangle_it4.86.687610
X-RAY DIFFRACTIONr_mcangle_other4.7976.694611
X-RAY DIFFRACTIONr_scbond_it4.0854.86526
X-RAY DIFFRACTIONr_scbond_other3.9894.803519
X-RAY DIFFRACTIONr_scangle_it5.7657.206797
X-RAY DIFFRACTIONr_scangle_other5.6337.122786
X-RAY DIFFRACTIONr_lrange_it8.30254.6651123
X-RAY DIFFRACTIONr_lrange_other8.28854.6881123
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.1-2.1540.382250.3756560.3756810.7120.7921000.359
2.154-2.2130.41380.3516090.3546670.8430.81497.00150.333
2.213-2.2770.623220.6034510.6046420.5830.65873.6760.598
2.277-2.3470.388340.3375800.3396140.8230.8491000.308
2.347-2.4240.269290.2935800.2916090.9420.8891000.272
2.424-2.5090.3280.2865640.2875920.920.9071000.249
2.509-2.6030.373370.2755280.285650.8510.9291000.243
2.603-2.7090.276300.2425170.2435480.9550.94999.81750.209
2.709-2.8290.357250.1794970.1865220.9270.9721000.148
2.829-2.9660.209160.1774920.1785080.9770.9771000.155
2.966-3.1260.139270.1664680.1644950.9880.9811000.147
3.126-3.3140.164220.1424340.1434560.9850.9851000.127
3.314-3.5410.244220.1614140.1654360.9660.9831000.15
3.541-3.8230.235150.1893770.1914120.9630.97495.14560.171
3.823-4.1840.233150.1513600.1533780.9650.98399.20630.141
4.184-4.6720.156180.1513230.1513410.9870.9871000.153
4.672-5.3840.153160.1513000.1513160.9830.9861000.156
5.384-6.5670.249150.2012580.2042730.9680.9711000.196
6.567-9.1750.24680.1982120.22200.9130.9721000.21
9.175-41.8620.50670.2691370.2771440.8210.9321000.273

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