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- PDB-8ojx: Streptavidin S112YK121E artificial metalloenzyme for carboamination -

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Basic information

Entry
Database: PDB / ID: 8ojx
TitleStreptavidin S112YK121E artificial metalloenzyme for carboamination
ComponentsStreptavidin
KeywordsUNKNOWN FUNCTION / Streptavidin / Biotin / 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-0OD / : / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsIgareta, N.V. / Ward, T.R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Not funded Switzerland
CitationJournal: To Be Published
Title: Streptavidin WT artificial metalloenzyme for carboamination
Authors: Igareta, N.V.
History
DepositionMar 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 2.0Sep 2, 2026Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / pdbx_entry_details ...chem_comp / pdbx_entry_details / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _chem_comp.formula / _pdbx_entry_details.has_protein_modification
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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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)14,1645
Polymers12,9881
Non-polymers1,1764
Water1,49583
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,65820
Polymers51,9524
Non-polymers4,70616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
Buried area11610 Å2
ΔGint-136 kcal/mol
Surface area17740 Å2
Unit cell
Length a, b, c (Å)57.552, 57.552, 183.993
Angle α, β, γ (deg.)90, 90, 90
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-327-

HOH

21A-374-

HOH

31A-376-

HOH

41A-381-

HOH

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Components

#1: Protein Streptavidin


Mass: 12987.951 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-0OD / trichloro{(1,2,3,4,5-eta)-1,2,3,4-tetramethyl-5-[2-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)ethyl]cyclopentadienyl}rhodium(1+) / [Cp*(Biot-methylene)RhCl(H2O)2]+


Mass: 599.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H32Cl3N3O2RhS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ir
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 46.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 2 M ammonium sulfate 0.1 M sodium acetate pH 4.0 -> for soaking pH adjustment to 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: 1.00004 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: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.6→46.041 Å / Num. obs: 21012 / % possible obs: 100 % / Redundancy: 25.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.018 / Rrim(I) all: 0.068 / Net I/σ(I): 29.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.76-4620.10.04834830.9990.0130.05
1.6-1.6326.41.077269210.9290.31.118

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→46.041 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.179 / SU B: 1.289 / SU ML: 0.045 / Average fsc free: 0.9738 / Average fsc work: 0.9799 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1968 1040 4.963 %
Rwork0.1713 19914 -
all0.173 --
obs-20954 99.848 %
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: 28.867 Å2
Baniso -1Baniso -2Baniso -3
1--0.615 Å20 Å2-0 Å2
2---0.615 Å2-0 Å2
3---1.231 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms919 0 33 83 1035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.012990
X-RAY DIFFRACTIONr_bond_other_d0.0010.016821
X-RAY DIFFRACTIONr_angle_refined_deg2.1131.8331386
X-RAY DIFFRACTIONr_angle_other_deg0.6671.731871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4745125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.29654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49310124
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.6621043
X-RAY DIFFRACTIONr_chiral_restr0.1030.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021213
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02244
X-RAY DIFFRACTIONr_nbd_refined0.190.2167
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2080.2701
X-RAY DIFFRACTIONr_nbtor_refined0.1970.2473
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2506
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.248
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1650.226
X-RAY DIFFRACTIONr_nbd_other0.140.2108
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0980.220
X-RAY DIFFRACTIONr_mcbond_it2.6732.697495
X-RAY DIFFRACTIONr_mcbond_other2.6712.701496
X-RAY DIFFRACTIONr_mcangle_it3.914.835621
X-RAY DIFFRACTIONr_mcangle_other3.9084.839622
X-RAY DIFFRACTIONr_scbond_it4.1113.057495
X-RAY DIFFRACTIONr_scbond_other3.7482.939459
X-RAY DIFFRACTIONr_scangle_it6.1525.598745
X-RAY DIFFRACTIONr_scangle_other5.4285.22689
X-RAY DIFFRACTIONr_lrange_it7.72528.7421095
X-RAY DIFFRACTIONr_lrange_other7.43928.011065
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
1.6-1.6420.227520.21314610.21315130.9540.9661000.187
1.642-1.6860.226700.18613990.18814690.9710.9751000.16
1.686-1.7350.18650.1813820.1814470.9720.9781000.152
1.735-1.7890.236780.16413300.16714080.9680.9821000.142
1.789-1.8470.204810.16812780.1713590.9730.9821000.147
1.847-1.9120.207660.16612330.16813060.9720.98299.4640.146
1.912-1.9840.235650.1712130.17412850.9670.97999.45530.151
1.984-2.0650.168590.16611680.16612270.9830.9831000.151
2.065-2.1560.18650.14911180.15111830.9790.9861000.14
2.156-2.2610.213560.1710610.17211260.9760.98199.20070.158
2.261-2.3830.246470.16410380.16710900.9670.98399.54130.157
2.383-2.5280.147530.1619750.1610280.9860.9831000.157
2.528-2.7010.192420.1639180.1649600.9820.9841000.166
2.701-2.9170.219550.1628570.1659120.9720.9831000.171
2.917-3.1940.192420.1698080.178500.9760.9821000.186
3.194-3.5690.182360.1627260.1637630.9810.98499.86890.186
3.569-4.1170.14460.1576410.1566890.9890.98699.70970.184
4.117-5.0320.188330.1465580.1485910.9740.9881000.18
5.032-7.0750.179170.2174570.2164740.9820.9741000.273
7.075-46.0410.466120.2582930.2663050.9490.9451000.336

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