[English] 日本語
Yorodumi
- PDB-6sok: Engineered streptavidin variant (VTAR) in complex with the Twin-S... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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: 0 / Refine code: 0

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

-
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 / Amine


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more