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Basic information

Entry
Database: PDB / ID: 6ud6
TitleSpectroscopic and structural characterization of a genetically encoded direct sensor for protein-ligand interactions
ComponentsStreptavidin
KeywordsFLUORESCENT PROTEIN / unnatural amino acid / non-canonical amino acid / fluorescence / biosensor / small molecule biosensor / ligand detection
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: 1.502 Å
AuthorsMills, J.H. / Gleason, P.R. / Simmons, C.R. / Henderson, J.N. / Kartchner, B.K.
CitationJournal: Biochemistry / Year: 2021
Title: Structural Origins of Altered Spectroscopic Properties upon Ligand Binding in Proteins Containing a Fluorescent Noncanonical Amino Acid.
Authors: Gleason, P.R. / Kolbaba-Kartchner, B. / Henderson, J.N. / Stahl, E.P. / Simmons, C.R. / Mills, J.H.
History
DepositionSep 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,80111
Polymers29,0852
Non-polymers7169
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-40 kcal/mol
Surface area10970 Å2
MethodPISA
2
A: Streptavidin
B: Streptavidin
hetero molecules

A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,60222
Polymers58,1714
Non-polymers1,43118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1,z1
Buried area13130 Å2
ΔGint-96 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.519, 57.519, 173.026
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-397-

HOH

21A-400-

HOH

31B-345-

HOH

41B-393-

HOH

51B-410-

HOH

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Components

#1: Protein Streptavidin


Mass: 14542.706 Da / Num. of mol.: 2
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 500 ul of 0.1 M citric acid, pH 3.5, 3M NaCl in the reservoir with 2 ul of reservoir buffer mixed with 2 ul of 10 mg/ml of protein in the drop. Crystals were soaked to pH 5.5 overnight with 3 exchanges

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→29.631 Å / Num. obs: 44561 / % possible obs: 99.97 % / Redundancy: 13.5 % / CC1/2: 1 / Net I/σ(I): 14
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2228 / CC1/2: 0.845 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RY2

3ry2


Resolution: 1.502→29.631 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.32
RfactorNum. reflection% reflection
Rfree0.1904 1975 4.43 %
Rwork0.1727 --
obs0.1736 44553 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.59 Å2 / Biso mean: 24.2635 Å2 / Biso min: 11.44 Å2
Refinement stepCycle: final / Resolution: 1.502→29.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 90 223 2109
Biso mean--38.88 32.38 -
Num. residues----241
LS refinement shellResolution: 1.502→1.53 Å /
Num. reflection% reflection
Rwork2228 -
obs-100 %

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