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- PDB-6sok: Engineered streptavidin variant (VTAR) in complex with the Twin-S... -

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Basic information

Entry
Database: PDB / ID: 6sok
TitleEngineered streptavidin variant (VTAR) in complex with the Twin-Strep-tag peptide
Components
  • Streptavidin
  • Twin-Strep-tag peptide
KeywordsPEPTIDE BINDING PROTEIN / LOOP ENGINEERING / PROTEIN ENGINEERING / STREP-TAG / STREPTAVIDIN
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
AMINO GROUP / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å
AuthorsSkerra, A. / Eichinger, A.
CitationJournal: J.Mol.Biol. / Year: 2021
Title: The Role of Changing Loop Conformations in Streptavidin Versions Engineered for High-affinity Binding of the Strep-tag II Peptide.
Authors: Schmidt, T.G.M. / Eichinger, A. / Schneider, M. / Bonet, L. / Carl, U. / Karthaus, D. / Theobald, I. / Skerra, A.
History
DepositionAug 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 7, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Jan 24, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
P: Twin-Strep-tag peptide
Q: Twin-Strep-tag peptide
R: Twin-Strep-tag peptide
S: Twin-Strep-tag peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,26412
Polymers66,2008
Non-polymers644
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13800 Å2
ΔGint-71 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.340, 101.340, 118.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALYSLYSAA15 - 1343 - 122
21ALAALALYSLYSBB15 - 1343 - 122
12ALAALALYSLYSAA15 - 1343 - 122
22ALAALALYSLYSCC15 - 1343 - 122
13ALAALAPROPROAA15 - 1353 - 123
23ALAALAPROPRODD15 - 1353 - 123
14GLUGLUPROPROBB14 - 1352 - 123
24GLUGLUPROPROCC14 - 1352 - 123
15GLUGLULYSLYSBB14 - 1342 - 122
25GLUGLULYSLYSDD14 - 1342 - 122
16GLUGLULYSLYSCC14 - 1342 - 122
26GLUGLULYSLYSDD14 - 1342 - 122

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Streptavidin


Mass: 13383.561 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: engineered protein / Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Protein/peptide
Twin-Strep-tag peptide


Mass: 3166.316 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: The peptide SAWSHPQFEKGGGSGGGSGGSAWSHPQFEK carries an anthraniloyl/2-aminobenzoyl (BE2) group at the N-terminus and an amide group at the C-terminus.
Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NH2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: ammonium sulfate, sodium citrate-phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2015 / Details: Si mirror
RadiationMonochromator: Si 111 Double-Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.96→76.973 Å / Num. obs: 44784 / % possible obs: 99.9 % / Redundancy: 10 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.069 / Rsym value: 0.066 / Net I/av σ(I): 9.6 / Net I/σ(I): 22.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.96-2.0710.60.2812.764190.0890.2950.28199.7
2.07-2.1910.10.2113.660820.0690.2220.21199.9
2.19-2.349.70.1744.357350.0580.1830.17499.9
2.34-2.5310.40.1465.153540.0470.1530.146100
2.53-2.779.60.1057.149580.0350.1110.105100
2.77-3.110.30.0721045070.0230.0760.072100
3.1-3.589.90.0461539840.0150.0480.04699.9
3.58-4.3910.20.03220.434280.010.0330.032100
4.39-6.29.50.02722.327150.0090.0290.027100
6.2-76.9739.10.02510.816020.010.0270.025100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.47 Å46.58 Å
Translation7.47 Å46.58 Å

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Processing

Software
NameVersionClassification
MOSFLM7.1.3data reduction
SCALA3.3.22data scaling
PHASER2.5.7phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QBB

6qbb


Resolution: 1.96→76.97 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.715 / SU ML: 0.069 / SU R Cruickshank DPI: 0.1216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.115
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1838 2130 4.8 %RANDOM
Rwork0.1515 ---
obs0.1531 42601 99.86 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 132.1 Å2 / Biso mean: 28.404 Å2 / Biso min: 10.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2---0.48 Å20 Å2
3---0.95 Å2
Refinement stepCycle: final / Resolution: 1.96→76.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3920 0 4 242 4166
Biso mean--67.3 31.33 -
Num. residues----519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0124050
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183503
X-RAY DIFFRACTIONr_angle_refined_deg2.1481.6525543
X-RAY DIFFRACTIONr_angle_other_deg1.671.5818090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2225521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.76322.083192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49415560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2011520
X-RAY DIFFRACTIONr_chiral_restr0.1120.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.024668
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02928
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A35940.1
12B35940.1
21A36740.09
22C36740.09
31A37160.09
32D37160.09
41B36910.1
42C36910.1
51B36720.09
52D36720.09
61C37620.08
62D37620.08
LS refinement shellResolution: 1.961→2.012 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 151 -
Rwork0.164 3084 -
all-3235 -
obs--99.32 %
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)
10.9170.0208-0.0060.82980.18150.6255-0.0433-0.158-0.19540.0373-0.03550.015-0.0105-0.08180.07880.04370.024-0.00250.07850.03730.063326.77966.3646.936
20.8509-0.15010.16640.2105-0.18430.7954-0.04880.0527-0.0065-0.0874-0.08-0.0968-0.08970.03510.12880.09610.03660.03930.05960.01680.069636.28374.247-5.244
30.29240.131-0.13911.0766-0.27240.37960.0021-0.1251-0.02940.0599-0.00830.0477-0.0724-0.01560.00620.04910.015-0.00620.0787-0.0050.062812.05390.3217.477
40.78490.1056-0.2990.16830.0050.5865-0.04420.0197-0.0365-0.15820.01050.0393-0.0689-0.01240.03370.1568-0.0068-0.03990.01880.00840.050113.43990.423-9.645
514.68547.2666-5.295513.5738-3.90914.70220.14550.5615-0.54080.2104-0.06840.9840.6734-0.7321-0.07710.2625-0.02820.01360.2556-0.03580.364416.27662.6981.421
67.2843-0.4255-3.83637.7367-0.732614.8625-0.1580.11070.6873-0.11860.48420.1526-0.59380.5702-0.32620.2677-0.0454-0.06160.39190.1710.436240.11784.224-1.215
72.4128-1.57530.75014.24573.505915.2517-0.0999-0.10350.20970.37950.1074-0.36450.30270.1328-0.00740.1986-0.0094-0.0590.1678-0.03290.151623.06693.85614.025
82.2512-3.0436-0.73034.29470.157818.35970.01590.1763-0.2576-0.0695-0.04170.35190.3820.20380.02580.1858-0.0302-0.0490.3271-0.03710.17059.80579.272-15.062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 137
2X-RAY DIFFRACTION2B14 - 135
3X-RAY DIFFRACTION3C14 - 135
4X-RAY DIFFRACTION4D13 - 135
5X-RAY DIFFRACTION5E3 - 11
6X-RAY DIFFRACTION6F1 - 11
7X-RAY DIFFRACTION7G3 - 11
8X-RAY DIFFRACTION8H3 - 11

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