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- PDB-6udb: Spectroscopic and structural characterization of a genetically en... -

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Basic information

Entry
Database: PDB / ID: 6udb
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
DI(HYDROXYETHYL)ETHER / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 19, 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)58,8888
Polymers58,4634
Non-polymers4244
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10110 Å2
ΔGint-38 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.458, 85.555, 58.098
Angle α, β, γ (deg.)90.000, 99.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Streptavidin


Mass: 14615.757 Da / Num. of mol.: 4
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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 500 ul of 0.1 M Bis-Tris, pH 6.5, 25% w/v polyethylene glycol 3350 in the reservoir with 2 ul of reservoir buffer mixed with 2 ul of 10 mg/ml of protein in the drop

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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: Feb 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→42.78 Å / Num. obs: 64849 / % possible obs: 99.6 % / Redundancy: 1 % / CC1/2: 0.923 / Net I/σ(I): 10.9
Reflection shellResolution: 1.55→1.58 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3014 / CC1/2: 0.938

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RY2

3ry2


Resolution: 1.55→42.78 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.046 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.082 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 2000 3.1 %RANDOM
Rwork0.1659 ---
obs0.167 62823 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.22 Å2 / Biso mean: 28.433 Å2 / Biso min: 13.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.31 Å2
2--1.85 Å20 Å2
3----1.78 Å2
Refinement stepCycle: final / Resolution: 1.55→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3590 0 28 451 4069
Biso mean--41.59 40.71 -
Num. residues----483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.023905
X-RAY DIFFRACTIONr_angle_refined_deg2.1471.9145400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.285542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.47323.537147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68615507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6731515
X-RAY DIFFRACTIONr_chiral_restr0.1720.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023021
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.292 141 -
Rwork0.28 4450 -
obs--95.31 %

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