[English] 日本語
Yorodumi
- PDB-6gwa: Concanavalin B structure determined with data from the EuXFEL, th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gwa
TitleConcanavalin B structure determined with data from the EuXFEL, the first MHz free electron laser
ComponentsConcanavalin B
KeywordsSUGAR BINDING PROTEIN / Free-electron laser / serial crystallography / lectin
Function / homology
Function and homology information


hydrolase activity / carbohydrate metabolic process
Similarity search - Function
Chitinase Cts1-like / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGruenbein, M.L. / Gorel, A. / Stricker, M. / Bean, R. / Bielecki, J. / Doerner, K. / Hartmann, E. / Hilpert, M. / Kloos, M. / Letrun, R. ...Gruenbein, M.L. / Gorel, A. / Stricker, M. / Bean, R. / Bielecki, J. / Doerner, K. / Hartmann, E. / Hilpert, M. / Kloos, M. / Letrun, R. / Sztuk-Dambietz, J. / Mancuso, A. / Meserschmidt, M. / Nass-Kovacs, G. / Ramilli, M. / Roome, C.M. / Sato, T. / Doak, R.B. / Shoeman, R.L. / Foucar, L. / Colletier, J.P. / Barends, T.R.M. / Stan, C. / Schlichting, I.
CitationJournal: Nat Commun / Year: 2018
Title: Megahertz data collection from protein microcrystals at an X-ray free-electron laser.
Authors: Grunbein, M.L. / Bielecki, J. / Gorel, A. / Stricker, M. / Bean, R. / Cammarata, M. / Dorner, K. / Frohlich, L. / Hartmann, E. / Hauf, S. / Hilpert, M. / Kim, Y. / Kloos, M. / Letrun, R. / ...Authors: Grunbein, M.L. / Bielecki, J. / Gorel, A. / Stricker, M. / Bean, R. / Cammarata, M. / Dorner, K. / Frohlich, L. / Hartmann, E. / Hauf, S. / Hilpert, M. / Kim, Y. / Kloos, M. / Letrun, R. / Messerschmidt, M. / Mills, G. / Nass Kovacs, G. / Ramilli, M. / Roome, C.M. / Sato, T. / Scholz, M. / Sliwa, M. / Sztuk-Dambietz, J. / Weik, M. / Weinhausen, B. / Al-Qudami, N. / Boukhelef, D. / Brockhauser, S. / Ehsan, W. / Emons, M. / Esenov, S. / Fangohr, H. / Kaukher, A. / Kluyver, T. / Lederer, M. / Maia, L. / Manetti, M. / Michelat, T. / Munnich, A. / Pallas, F. / Palmer, G. / Previtali, G. / Raab, N. / Silenzi, A. / Szuba, J. / Venkatesan, S. / Wrona, K. / Zhu, J. / Doak, R.B. / Shoeman, R.L. / Foucar, L. / Colletier, J.P. / Mancuso, A.P. / Barends, T.R.M. / Stan, C.A. / Schlichting, I.
History
DepositionJun 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.3Jan 17, 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: Concanavalin B


Theoretical massNumber of molelcules
Total (without water)33,8661
Polymers33,8661
Non-polymers00
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.250, 82.250, 103.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Concanavalin B / Con B


Mass: 33866.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P49347
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.74 %
Crystal growTemperature: 293 K / Method: batch mode / Details: Batch mode, acetone

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.66 Å
DetectorType: AGIPD / Detector: PIXEL / Date: Jun 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.66 Å / Relative weight: 1
ReflectionResolution: 2.1→42 Å / Num. obs: 23105 / % possible obs: 100 % / Redundancy: 650 % / R split: 0.164 / Net I/σ(I): 6.9
Reflection shellResolution: 2.1→2.2 Å / R split: 0.876

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CNV

1cnv


Resolution: 2.1→41.841 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 21.34
RfactorNum. reflection% reflection
Rfree0.2188 1152 4.99 %
Rwork0.162 --
obs0.1647 23105 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→41.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2265 0 0 159 2424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092336
X-RAY DIFFRACTIONf_angle_d1.1393168
X-RAY DIFFRACTIONf_dihedral_angle_d14.565860
X-RAY DIFFRACTIONf_chiral_restr0.046337
X-RAY DIFFRACTIONf_plane_restr0.004413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.19560.31641570.27132663X-RAY DIFFRACTION97
2.1956-2.31130.2881600.21912719X-RAY DIFFRACTION100
2.3113-2.45610.23861390.19142741X-RAY DIFFRACTION100
2.4561-2.64580.25421260.18812776X-RAY DIFFRACTION100
2.6458-2.9120.22911410.17892729X-RAY DIFFRACTION100
2.912-3.33320.24331450.16682757X-RAY DIFFRACTION100
3.3332-4.19880.17981530.13262756X-RAY DIFFRACTION100
4.1988-41.8490.16441310.12042812X-RAY DIFFRACTION100

+
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