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- PDB-6gw9: Concanavalin A structure determined with data from the EuXFEL, th... -

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Basic information

Entry
Database: PDB / ID: 6gw9
TitleConcanavalin A structure determined with data from the EuXFEL, the first MHz free electron laser
ComponentsConcanavalin V
KeywordsSUGAR BINDING PROTEIN / Free-electron laser / serial crystallography / lectin
Function / homology
Function and homology information


glucose binding / mannose binding / vasodilation / manganese ion binding / calcium ion binding
Similarity search - Function
Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCanavalia cathartica (xiao dao dou)
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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Concanavalin V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6873
Polymers25,6221
Non-polymers642
Water1,29772
1
A: Concanavalin V
hetero molecules

A: Concanavalin V
hetero molecules

A: Concanavalin V
hetero molecules

A: Concanavalin V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,74712
Polymers102,4904
Non-polymers2588
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area8480 Å2
ΔGint-120 kcal/mol
Surface area34580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.800, 88.100, 90.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

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Components

#1: Protein Concanavalin V / ConV


Mass: 25622.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canavalia cathartica (xiao dao dou) / References: UniProt: C0HJY1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 293 K / Method: batch mode / Details: batch crystallization, acetone

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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→45 Å / Num. obs: 15227 / % possible obs: 100 % / Redundancy: 715 % / R split: 0.128 / Net I/σ(I): 7.2
Reflection shellResolution: 2.1→2.2 Å / Mean I/σ(I) obs: 2 / R split: 0.694

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Processing

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

1jbc


Resolution: 2.1→45 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 24.92
RfactorNum. reflection% reflection
Rfree0.2382 708 4.65 %
Rwork0.186 --
obs0.1883 15227 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1777 0 2 72 1851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021823
X-RAY DIFFRACTIONf_angle_d0.5772477
X-RAY DIFFRACTIONf_dihedral_angle_d8.836639
X-RAY DIFFRACTIONf_chiral_restr0.023285
X-RAY DIFFRACTIONf_plane_restr0.002319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.098-2.260.36671450.292830X-RAY DIFFRACTION99
2.26-2.48740.30941470.24592849X-RAY DIFFRACTION100
2.4874-2.84730.28591210.22772906X-RAY DIFFRACTION100
2.8473-3.58710.23881330.18122918X-RAY DIFFRACTION100
3.5871-45.11040.17661620.13773016X-RAY DIFFRACTION100

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