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- PDB-9qnp: Streptavidin K121W with a thiophenol cofactor as artificial hydro... -

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Basic information

Entry
Database: PDB / ID: 9qnp
TitleStreptavidin K121W with a thiophenol cofactor as artificial hydrogen atom transferase
ComponentsStreptavidin
KeywordsTRANSFERASE / Hydrogen atom transfer / thiophenol / streptavidin
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
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhang, K. / Ward, T.R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation200020_212088 Switzerland
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: An Asymmetric Hydrogen Atom Transferase with an Abiological Thiophenol Cofactor.
Authors: Cao, H. / Zhang, K. / Gorbachev, V. / Vornholt, T. / Yu, K. / Chen, D. / Ward, T.R.
History
DepositionMar 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: 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
B: Streptavidin
C: Streptavidin
D: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9108
Polymers66,5044
Non-polymers1,4064
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9400 Å2
ΔGint-55 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.245, 89.026, 57.891
Angle α, β, γ (deg.)90.00, 96.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-320-

HOH

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Components

#1: Protein
Streptavidin


Mass: 16626.061 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22629
#2: Chemical
ChemComp-A1I7Y / 5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(3-sulfanylphenyl)pentanamide


Mass: 351.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H21N3O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.23 Å3/Da / Density % sol: 44.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10 % w/v PEG 1K, 10 % w/v PEG 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6199 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 2.3→43.22 Å / Num. obs: 25882 / % possible obs: 99.9 % / Redundancy: 2 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.06073 / Rpim(I) all: 0.06073 / Rrim(I) all: 0.08589 / Net I/σ(I): 9.28
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4825 / Mean I/σ(I) obs: 1.71 / Num. unique obs: 2577 / CC1/2: 0.694 / CC star: 0.905 / Rpim(I) all: 0.4825 / Rrim(I) all: 0.6824 / % possible all: 99.92

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→43.22 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.399 / SU ML: 0.197 / Cross valid method: FREE R-VALUE / ESU R: 0.308 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.25388 1258 4.9 %
Rwork0.19737 --
obs0.2001 24626 99.9 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.262 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0.01 Å2
2---0.02 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.3→43.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3767 0 92 81 3940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123966
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163438
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.7855430
X-RAY DIFFRACTIONr_angle_other_deg0.5941.7597861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0385497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.865520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48910512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024926
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021018
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_it4.2944.3742000
X-RAY DIFFRACTIONr_mcbond_other4.2934.3742000
X-RAY DIFFRACTIONr_mcangle_it6.5547.8282493
X-RAY DIFFRACTIONr_mcangle_other6.5527.8292494
X-RAY DIFFRACTIONr_scbond_it4.7584.731966
X-RAY DIFFRACTIONr_scbond_other4.7574.731967
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1448.4872938
X-RAY DIFFRACTIONr_long_range_B_refined10.07743.324415
X-RAY DIFFRACTIONr_long_range_B_other10.08143.354410
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 94 -
Rwork0.29 1814 -
obs--100 %

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