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- PDB-9qne: Streptavidin with a thiophenol cofactor as artificial hydrogen at... -

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Basic information

Entry
Database: PDB / ID: 9qne
TitleStreptavidin 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: 1.84 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 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)17,2938
Polymers16,5691
Non-polymers7247
Water1,71195
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,17232
Polymers66,2764
Non-polymers2,89628
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
Unit cell
Length a, b, c (Å)57.388, 57.388, 182.440
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-325-

HOH

21A-387-

HOH

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Components

#1: Protein Streptavidin


Mass: 16569.031 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: C16H21N3O2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M MES pH 5.5, 25 % w/v PEG 4K, 0.15 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.84→41.74 Å / Num. obs: 13751 / % possible obs: 99.89 % / Redundancy: 2 % / CC1/2: 1 / Rmerge(I) obs: 0.025 / Rpim(I) all: 0.025 / Rrim(I) all: 0.035 / Net I/σ(I): 15.24
Reflection shellResolution: 1.84→1.906 Å / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1331 / CC1/2: 0.91 / CC star: 0.976 / Rpim(I) all: 0.258 / Rrim(I) all: 0.365

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→41.74 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.669 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.112 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.20164 700 5.1 %
Rwork0.16518 --
obs0.16707 13051 99.99 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.643 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0 Å2
2--0.04 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.84→41.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 47 95 1078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121056
X-RAY DIFFRACTIONr_bond_other_d0.0020.017939
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.8211431
X-RAY DIFFRACTIONr_angle_other_deg0.6221.7762153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6445130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.68156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98910138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021287
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02269
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_it2.8072.744514
X-RAY DIFFRACTIONr_mcbond_other2.8022.743514
X-RAY DIFFRACTIONr_mcangle_it4.1134.892646
X-RAY DIFFRACTIONr_mcangle_other4.1124.901647
X-RAY DIFFRACTIONr_scbond_it3.5863.041542
X-RAY DIFFRACTIONr_scbond_other3.5823.046543
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3345.343786
X-RAY DIFFRACTIONr_long_range_B_refined7.94529.821187
X-RAY DIFFRACTIONr_long_range_B_other7.93729.841183
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 52 -
Rwork0.264 937 -
obs--100 %

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