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- PDB-6xt6: pro-concanavalin A: Precursor of circularly permuted concanavalin A -

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Basic information

Entry
Database: PDB / ID: 6xt6
Titlepro-concanavalin A: Precursor of circularly permuted concanavalin A
ComponentsConcanavalin-A
KeywordsPLANT PROTEIN / Lectin / Carbohydrate-binding
Function / homology
Function and homology information


regulation of defense response to virus / D-mannose binding / defense response / metal ion binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.103 Å
AuthorsNonis, S.G. / Haywood, J. / Schmidberger, J.W. / Bond, C.S.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP160100107 Australia
Australian Research Council (ARC)DE180101445 Australia
Citation
Journal: Plant Cell / Year: 2021
Title: Structural and biochemical analyses of concanavalin A circular permutation by jack bean asparaginyl endopeptidase.
Authors: Nonis, S.G. / Haywood, J. / Schmidberger, J.W. / Mackie, E.R.R. / Soares da Costa, T.P. / Bond, C.S. / Mylne, J.S.
#1: Journal: Biorxiv / Year: 2020
Title: Structural basis for a natural circular permutation in proteins
Authors: Nonis, S.G. / Haywood, J. / Schmidberger, J.W. / Bond, C.S. / Mylne, J.S.
History
DepositionJul 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 29, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Concanavalin-A
B: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,81725
Polymers56,4852
Non-polymers1,33223
Water1,44180
1
A: Concanavalin-A
B: Concanavalin-A
hetero molecules

A: Concanavalin-A
B: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,63350
Polymers112,9694
Non-polymers2,66446
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area14630 Å2
ΔGint-185 kcal/mol
Surface area34910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.939, 90.420, 86.863
Angle α, β, γ (deg.)90.000, 91.128, 90.000
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Concanavalin-A / Con A


Mass: 28242.283 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canavalia ensiformis (jack bean) / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle Express / References: UniProt: P02866

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Non-polymers , 5 types, 103 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.09 Å3/Da / Density % sol: 41.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: Zinc chloride, HEPES, PEG 6000 / PH range: 6.8 - 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.1→48.885 Å / Num. obs: 26657 / % possible obs: 98.8 % / Redundancy: 3.4 % / CC1/2: 0.994 / Net I/σ(I): 6.5
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 2045 / CC1/2: 0.743

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JBC

1jbc


Resolution: 2.103→48.885 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.178 / SU B: 6.582 / SU ML: 0.167 / Average fsc free: 0.8829 / Average fsc work: 0.8999 / Cross valid method: FREE R-VALUE / ESU R: 0.254 / ESU R Free: 0.204
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2441 1307 4.905 %
Rwork0.1908 25340 -
all0.193 --
obs-26647 98.791 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.506 Å2
Baniso -1Baniso -2Baniso -3
1-1.672 Å20 Å21.335 Å2
2---2.213 Å20 Å2
3---0.488 Å2
Refinement stepCycle: LAST / Resolution: 2.103→48.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3677 0 68 80 3825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133829
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173471
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.6395192
X-RAY DIFFRACTIONr_angle_other_deg1.2451.5738077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9155482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56623.895172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39915590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7841512
X-RAY DIFFRACTIONr_chiral_restr0.0640.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024258
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02758
X-RAY DIFFRACTIONr_nbd_refined0.1980.2660
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.23265
X-RAY DIFFRACTIONr_nbtor_refined0.1610.21785
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21737
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2161
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1910.222
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3050.230
X-RAY DIFFRACTIONr_nbd_other0.2550.289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2370.213
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2620.21
X-RAY DIFFRACTIONr_mcbond_it2.233.1341934
X-RAY DIFFRACTIONr_mcbond_other2.233.1331933
X-RAY DIFFRACTIONr_mcangle_it3.4084.6832414
X-RAY DIFFRACTIONr_mcangle_other3.4074.6832415
X-RAY DIFFRACTIONr_scbond_it2.7423.4341895
X-RAY DIFFRACTIONr_scbond_other2.7413.4351896
X-RAY DIFFRACTIONr_scangle_it4.1525.0112778
X-RAY DIFFRACTIONr_scangle_other4.1525.0122779
X-RAY DIFFRACTIONr_lrange_it6.11136.9574005
X-RAY DIFFRACTIONr_lrange_other6.10936.9574004
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.103-2.1580.327790.27917690.28119880.7570.7792.95770.267
2.158-2.2170.352960.26418310.26819350.7740.8199.58660.251
2.217-2.2810.286850.2317620.23218560.850.8899.51510.215
2.281-2.3510.28910.22717380.22918370.8490.87599.56450.211
2.351-2.4280.309940.2316610.23417650.8480.86999.43340.213
2.428-2.5130.292820.22516240.22917180.850.87199.30150.204
2.513-2.6070.294830.21215730.21616600.8840.90299.7590.191
2.607-2.7130.251850.19614940.19915910.9160.9299.24580.174
2.713-2.8340.231600.18914510.1915210.9110.9399.34250.169
2.834-2.9710.282480.1914060.19314600.8910.92699.5890.171
2.971-3.1310.233630.17413380.17614060.9180.9499.64440.158
3.131-3.3210.238890.17712300.18213290.930.93199.24760.165
3.321-3.5490.261610.17211410.17612170.910.9598.76750.16
3.549-3.8310.208590.1810900.18211640.9420.9498.71130.174
3.831-4.1940.22520.1619970.16410600.9470.96398.96230.157
4.194-4.6850.201470.149120.1439700.960.97198.8660.14
4.685-5.4020.224450.1648080.1678640.9460.96598.72690.163
5.402-6.5960.226240.1816830.1827170.9390.96498.60530.179
6.596-9.2440.184360.175260.1715700.9620.95798.59650.171
9.244-48.8850.209270.2533060.2493390.9510.93598.23010.283

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