[English] 日本語
Yorodumi
- PDB-6t1k: Streptavidin variants harbouring an artificial organocatalyst bas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t1k
TitleStreptavidin variants harbouring an artificial organocatalyst based cofactor
ComponentsStreptavidin
KeywordsBiotin-binding protein / artificial cofactor / streptavidin / catalyst
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
Chem-HL9 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLechner, H. / Hocker, B.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundJ 3994 Austria
CitationJournal: Chembiochem / Year: 2021
Title: An Artificial Cofactor Catalyzing the Baylis-Hillman Reaction with Designed Streptavidin as Protein Host*.
Authors: Lechner, H. / Emann, V.R. / Breuning, M. / Hocker, B.
History
DepositionOct 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0865
Polymers16,4961
Non-polymers5904
Water2,648147
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,34320
Polymers65,9844
Non-polymers2,35916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_555y,x,-z1
Buried area10420 Å2
ΔGint-42 kcal/mol
Surface area20230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.275, 57.275, 175.019
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-307-

HOH

21A-326-

HOH

-
Components

#1: Protein Streptavidin


Mass: 16495.938 Da / Num. of mol.: 1
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-HL9 / 5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(1-pyridin-4-ylpiperidin-4-yl)pentanamide


Mass: 403.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N5O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: CHES 0.1 M pH 9.5 30% PEG 3000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.2→43.75 Å / Num. obs: 46054 / % possible obs: 99.79 % / Redundancy: 10.7 % / Biso Wilson estimate: 14.78 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.47
Reflection shellResolution: 1.2→1.24 Å / Num. unique obs: 4461 / CC1/2: 0.301

-
Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T1E

6t1e


Resolution: 1.2→43.75 Å / SU ML: 0.145 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1909
RfactorNum. reflection% reflection
Rfree0.1709 2100 4.56 %
Rwork0.1565 --
obs0.1572 46044 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.63 Å2
Refinement stepCycle: LAST / Resolution: 1.2→43.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms913 0 40 147 1100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821130
X-RAY DIFFRACTIONf_angle_d1.15051561
X-RAY DIFFRACTIONf_chiral_restr0.2948165
X-RAY DIFFRACTIONf_plane_restr0.0069208
X-RAY DIFFRACTIONf_dihedral_angle_d14.6915652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.230.31591330.32642799X-RAY DIFFRACTION97.54
1.23-1.260.29161390.31152889X-RAY DIFFRACTION99.87
1.26-1.290.31031380.29532888X-RAY DIFFRACTION99.93
1.29-1.330.31991370.29642881X-RAY DIFFRACTION99.97
1.33-1.370.27161390.28262897X-RAY DIFFRACTION100
1.37-1.420.28621390.25142908X-RAY DIFFRACTION99.97
1.42-1.480.23351380.2162903X-RAY DIFFRACTION99.7
1.48-1.550.22371390.17872907X-RAY DIFFRACTION99.87
1.55-1.630.16181390.1572907X-RAY DIFFRACTION99.97
1.63-1.730.17311400.13952937X-RAY DIFFRACTION100
1.73-1.860.1441410.12732933X-RAY DIFFRACTION100
1.86-2.050.14361410.12592956X-RAY DIFFRACTION99.68
2.05-2.350.14161410.1232954X-RAY DIFFRACTION99.94
2.35-2.960.14781440.13593009X-RAY DIFFRACTION100
2.96-43.750.14791520.13953176X-RAY DIFFRACTION99.73
Refinement TLS params.Method: refined / Origin x: 13.9453499643 Å / Origin y: 24.4919537299 Å / Origin z: -3.090870903 Å
111213212223313233
T0.0852377750366 Å20.00355430230411 Å2-0.00973819648751 Å2-0.109653943724 Å20.0147119414964 Å2--0.108235888042 Å2
L1.06701954458 °2-0.0159378335032 °20.352588936374 °2-1.0476956485 °2-0.0780208588973 °2--1.08514431134 °2
S-0.00563885914798 Å °0.00114490049359 Å °-0.0094875395155 Å °-0.0188670968567 Å °0.071786956008 Å °0.099129278048 Å °-0.000570716595088 Å °-0.159883781108 Å °0.0112564662131 Å °
Refinement TLS groupSelection details: all

+
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