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- PDB-8by1: streptavidin with an iridium catalyst for CH activation -

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Basic information

Entry
Database: PDB / ID: 8by1
Titlestreptavidin 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: 1.486 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
Revision 1.1Dec 27, 2023Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3]

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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)14,1084
Polymers13,0681
Non-polymers1,0403
Water1,56787
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,43116
Polymers52,2734
Non-polymers4,15812
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 area10160 Å2
ΔGint-106 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.657, 57.657, 183.626
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-325-

HOH

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Components

#1: Protein Streptavidin


Mass: 13068.129 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.: 87 / 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: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 2 M ammonium sulfate 0.1 M sodium acetate (soaking at 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: Sep 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 1.486→45.949 Å / Num. obs: 26068 / % possible obs: 99.9 % / Redundancy: 25.3 % / CC1/2: 1 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.02 / Rrim(I) all: 0.076 / Net I/σ(I): 23.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.14-45.9120.60.0382100.9990.010.039
1.49-1.5119.42.23712410.5560.7222.357

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
REFMAC5.8.0352refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Cootmodel building
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BC3

2bc3


Resolution: 1.486→45.949 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.176 / SU B: 1.119 / SU ML: 0.042 / Average fsc free: 0.9709 / Average fsc work: 0.9766 / Cross valid method: NONE / ESU R: 0.061 / ESU R Free: 0.062
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1945 1366 5.271 %
Rwork0.1729 24547 -
all0.174 --
obs-25913 99.348 %
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: 24.472 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0 Å2-0 Å2
2---0.47 Å2-0 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.486→45.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 55 87 1066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121035
X-RAY DIFFRACTIONr_bond_other_d0.0090.016866
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.7671460
X-RAY DIFFRACTIONr_angle_other_deg0.6231.6411991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2935126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.90755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62810130
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.7081042
X-RAY DIFFRACTIONr_chiral_restr0.0860.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021171
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02214
X-RAY DIFFRACTIONr_nbd_refined0.2130.2140
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.2763
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2465
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2527
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0910.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2350.212
X-RAY DIFFRACTIONr_nbd_other0.1890.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.216
X-RAY DIFFRACTIONr_mcbond_it2.1622.442499
X-RAY DIFFRACTIONr_mcbond_other2.1612.447500
X-RAY DIFFRACTIONr_mcangle_it3.1823.658626
X-RAY DIFFRACTIONr_mcangle_other3.183.663627
X-RAY DIFFRACTIONr_scbond_it3.4213.026536
X-RAY DIFFRACTIONr_scbond_other3.2082.987529
X-RAY DIFFRACTIONr_scangle_it5.2944.436808
X-RAY DIFFRACTIONr_scangle_other4.9914.377797
X-RAY DIFFRACTIONr_lrange_it6.59132.2461122
X-RAY DIFFRACTIONr_lrange_other6.56830.5651107
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.486-1.5250.2931190.2661714X-RAY DIFFRACTION97.969
1.525-1.5670.215970.2151750X-RAY DIFFRACTION100
1.567-1.6120.223980.1981693X-RAY DIFFRACTION100
1.612-1.6620.208890.1771652X-RAY DIFFRACTION100
1.662-1.7160.188840.1721616X-RAY DIFFRACTION100
1.716-1.7760.197920.1591545X-RAY DIFFRACTION100
1.776-1.8430.166690.1581520X-RAY DIFFRACTION99.9371
1.843-1.9180.24900.1881405X-RAY DIFFRACTION97.8403
1.918-2.0030.195580.1781387X-RAY DIFFRACTION98.0326
2.003-2.1010.177870.1581318X-RAY DIFFRACTION100
2.101-2.2140.186630.1491281X-RAY DIFFRACTION100
2.214-2.3480.205670.1881148X-RAY DIFFRACTION95.2194
2.348-2.510.186690.1621145X-RAY DIFFRACTION100
2.51-2.710.191570.161064X-RAY DIFFRACTION99.8219
2.71-2.9680.174520.167985X-RAY DIFFRACTION100
2.968-3.3170.228470.163912X-RAY DIFFRACTION100
3.317-3.8260.186470.158807X-RAY DIFFRACTION99.6499
3.826-4.6780.13410.143689X-RAY DIFFRACTION100
4.678-6.5820.176250.178564X-RAY DIFFRACTION99.6616
6.582-45.9490.428150.287352X-RAY DIFFRACTION100

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