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- PDB-3t6l: Y54F mutant of core streptavidin -

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Basic information

Entry
Database: PDB / ID: 3t6l
TitleY54F mutant of core streptavidin
ComponentsStreptavidin
KeywordsBIOTIN BINDING PROTEIN
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin ...Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsBaugh, L. / Le Trong, I. / Stayton, P.S. / Stenkamp, R.E. / Lybrand, T.P.
CitationJournal: Biochemistry / Year: 2012
Title: Second-Contact Shell Mutation Diminishes Streptavidin-Biotin Binding Affinity through Transmitted Effects on Equilibrium Dynamics.
Authors: Baugh, L. / Le Trong, I. / Cerutti, D.S. / Mehta, N. / Gulich, S. / Stayton, P.S. / Stenkamp, R.E. / Lybrand, T.P.
History
DepositionJul 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3633
Polymers13,2651
Non-polymers982
Water2,018112
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,45112
Polymers53,0614
Non-polymers3908
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_556y,x,-z+11
Buried area10070 Å2
ΔGint-72 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.273, 57.273, 171.715
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-6001-

HOH

21A-6043-

HOH

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Components

#1: Protein Streptavidin


Mass: 13265.336 Da / Num. of mol.: 1 / Fragment: UNP residues 37-163 / Mutation: Y54F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P22629
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 2.5 M sodium chloride, 0.1 M sodium-potassium phosphate (30% ethylene glycol cryoprotectant), pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2011
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→36.628 Å / Num. all: 35684 / Num. obs: 35679 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 21.8
Reflection shellResolution: 1.15→1.21 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.967 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6957 / % possible all: 93.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MM9

1mm9


Resolution: 1.3→36.628 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.1554 / WRfactor Rwork: 0.1316 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9309 / SU B: 1 / SU ML: 0.02 / SU R Cruickshank DPI: 0.0387 / SU Rfree: 0.0384 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.039 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.16 1811 5.1 %RANDOM
Rwork0.1353 ---
all0.1366 33868 --
obs0.1366 33868 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 51.57 Å2 / Biso mean: 17.4686 Å2 / Biso min: 8.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.3→36.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms897 0 5 112 1014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211021
X-RAY DIFFRACTIONr_bond_other_d0.0010.02646
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.8941404
X-RAY DIFFRACTIONr_angle_other_deg1.02731577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5475132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.34923.86444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.83815148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.099155
X-RAY DIFFRACTIONr_chiral_restr0.1260.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021179
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02224
X-RAY DIFFRACTIONr_mcbond_it3.114637
X-RAY DIFFRACTIONr_mcbond_other2.4694269
X-RAY DIFFRACTIONr_mcangle_it4.29361033
X-RAY DIFFRACTIONr_scbond_it4.5656384
X-RAY DIFFRACTIONr_scangle_it6.0510371
X-RAY DIFFRACTIONr_rigid_bond_restr2.21731667
X-RAY DIFFRACTIONr_sphericity_free10.6793120
X-RAY DIFFRACTIONr_sphericity_bonded5.30531639
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 144 -
Rwork0.129 2450 -
all-2594 -
obs--100 %

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