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- PDB-4jo6: Streptavidin complex with SBP-Tag -

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Basic information

Entry
Database: PDB / ID: 4jo6
TitleStreptavidin complex with SBP-Tag
Components
  • SBP-Tag
  • Streptavidin
KeywordsUNKNOWN FUNCTION / Homotetramer bound to peptides / Biotechnological targeting / Biotin and peptide binding
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 / Resolution: 1.75 Å
AuthorsBarrette-Ng, I.H. / Wu, S.C. / Tjia, W.M. / Wong, S.L. / Ng, K.K.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The structure of the SBP-Tag-streptavidin complex reveals a novel helical scaffold bridging binding pockets on separate subunits
Authors: Barrette-Ng, I.H. / Wu, S.C. / Tjia, W.M. / Wong, S.L. / Ng, K.K.
History
DepositionMar 17, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Y: SBP-Tag
Z: SBP-Tag


Theoretical massNumber of molelcules
Total (without water)74,6476
Polymers74,6476
Non-polymers00
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14370 Å2
ΔGint-73 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.523, 57.523, 177.552
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Streptavidin


Mass: 16504.852 Da / Num. of mol.: 4 / Fragment: UNP residues 25-183 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Protein/peptide SBP-Tag


Mass: 4313.770 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The synthetic peptide was originally isolated from an in vitro selection and evolution experiment.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 56% Tacsimate, 12%(w/v) glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 18, 2008 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→60 Å / Num. obs: 52299 / % possible obs: 95.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 29.2
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.5 / Num. unique all: 14270 / Rsym value: 0.424 / % possible all: 72.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SWE

1swe


Resolution: 1.75→57.54 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.386 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24201 2777 5 %RANDOM
Rwork0.20618 ---
all0.20798 52299 --
obs0.20798 52299 95.26 %-
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 mean: 28.361 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2---0.56 Å20 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.75→57.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3979 0 0 273 4252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214069
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.8935555
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6125523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.03323.75176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96815561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5091520
X-RAY DIFFRACTIONr_chiral_restr0.0840.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023140
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.64122581
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6732.54079
X-RAY DIFFRACTIONr_scbond_it3.3973.51488
X-RAY DIFFRACTIONr_scangle_it4.854.51476
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 159 -
Rwork0.199 2943 -
obs--72.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7631-0.00820.12930.72210.01780.99450.0328-0.04010.0278-0.0160.06440.0877-0.18-0.0268-0.09720.13470.01520.00980.10280.0120.029514.6484.71524.833
20.8851-0.02550.22340.89980.15780.6240.01560.0581-0.0889-0.06940.1057-0.0390.00220.1764-0.12130.10860.0040.00220.1531-0.02230.036625.471-6.32418.972
30.8596-0.04210.14830.87190.32870.88830.1007-0.0808-0.03740.07220.0252-0.09510.210.004-0.12590.14530.0039-0.03040.09940.00730.02636.429-25.5324.239
40.76640.00920.1280.82180.19111.12650.06-0.02030.0818-0.04030.03510.0186-0.0321-0.2014-0.09510.10750.01560.01030.13620.01520.0326-4.709-14.65318.335
50.46050.4875-0.348618.51052.39968.41350.3217-0.27970.05891.0149-0.278-0.09460.1273-0.4054-0.04380.2836-0.13990.02280.3283-0.04890.017410.191-9.88238.663
611.59580.6433-1.18730.55690.58836.4891-0.41530.2902-0.2455-0.27380.3484-0.0953-0.17320.05810.0670.3139-0.10030.01240.2559-0.06170.066511.641-10.1854.699
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 134
2X-RAY DIFFRACTION2B15 - 134
3X-RAY DIFFRACTION3C15 - 135
4X-RAY DIFFRACTION4D15 - 134
5X-RAY DIFFRACTION5Y11 - 35
6X-RAY DIFFRACTION6Z11 - 35

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