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

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Basic information

Entry
Database: PDB / ID: 6udc
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
BIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.2Nov 13, 2024Group: Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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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)59,4408
Polymers58,4634
Non-polymers9774
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11510 Å2
ΔGint-36 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.812, 98.281, 52.647
Angle α, β, γ (deg.)90.000, 112.260, 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-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.1 Å3/Da / Density % sol: 41.43 %
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: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→49.14 Å / Num. obs: 26913 / % possible obs: 97.1 % / Redundancy: 1 % / CC1/2: 0.725 / Net I/σ(I): 8.1
Reflection shellResolution: 2.1→2.16 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2062 / CC1/2: 0.582 / % possible all: 92.6

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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 / Resolution: 2.1→49.14 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.094 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 2017 7.5 %RANDOM
Rwork0.1942 ---
obs0.1988 24877 96.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.47 Å2 / Biso mean: 38.704 Å2 / Biso min: 19.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å2-0.27 Å2
2---0.15 Å20 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 2.1→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3632 0 64 50 3746
Biso mean--33.18 33.33 -
Num. residues----481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023807
X-RAY DIFFRACTIONr_bond_other_d0.0020.023210
X-RAY DIFFRACTIONr_angle_refined_deg1.9191.9255221
X-RAY DIFFRACTIONr_angle_other_deg1.05637415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3225481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.1223.766154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.96315487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5661516
X-RAY DIFFRACTIONr_chiral_restr0.1070.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024378
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02866
LS refinement shellResolution: 2.104→2.158 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 141 -
Rwork0.287 1698 -
all-1839 -
obs--91.63 %

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