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- PDB-2yz4: The neutron structure of concanavalin A at 2.2 Angstroms -

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Basic information

Entry
Database: PDB / ID: 2yz4
TitleThe neutron structure of concanavalin A at 2.2 Angstroms
ComponentsConcanavalin A
KeywordsSUGAR BINDING PROTEIN / PROTONATION STATES
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, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Legume lectin / 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
DEUTERATED WATER / : / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodNEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAhmed, H.U. / Blakeley, M.P. / Cianci, M. / Hubbard, J.A. / Helliwell, J.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: The determination of protonation states in proteins.
Authors: Ahmed, H.U. / Blakeley, M.P. / Cianci, M. / Cruickshank, D.W. / Hubbard, J.A. / Helliwell, J.R.
History
DepositionMay 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Oct 11, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Refinement description / Source and taxonomy
Category: atom_site / entity_src_nat ...atom_site / entity_src_nat / pdbx_distant_solvent_atoms / software
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _software.classification / _software.name
Revision 2.1Oct 25, 2023Group: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Concanavalin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7173
Polymers25,6221
Non-polymers952
Water1,51384
1
A: Concanavalin A
hetero molecules

A: Concanavalin A
hetero molecules

A: Concanavalin A
hetero molecules

A: Concanavalin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,87012
Polymers102,4904
Non-polymers3808
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)89.377, 87.314, 63.051
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Concanavalin A / Con A


Mass: 25622.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: batch dialysis / pH: 6.5
Details: 0.1M NaNO3, 0.05M Tris-acetate, 1mM MnCl2, 1mM CaCl2, pH 6.5, BATCH DIALYSIS, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 2.9-3.9
DetectorType: IMAGE PLATE / Detector: LADI / Date: Jun 1, 2005
RadiationMonochromator: MULTI MIRROR BANDPASS FILTER / Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
12.91
23.91
ReflectionResolution: 2.181→33.653 Å / Num. all: 8512 / Num. obs: 8512 / % possible obs: 67.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.213 / Rsym value: 0.213 / Net I/σ(I): 2.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.3240.3141.934848610.31446.9
2.32-2.464.30.3132.137438620.31350.1
2.46-2.634.40.2922.337408550.29252.4
2.63-2.844.70.2892.341848870.28959
2.84-3.115.50.2592.652269560.25969.5
3.11-3.486.90.2412.7708010320.24181
3.48-4.028.60.2233859810050.22390.1
4.02-4.929.60.1972.987259090.19794.3
4.92-6.9680.1513.858327290.15196.1
6.96-33.655.20.1144.521474160.11494.3

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
LADISPECdata collection
LAUEGENdata reduction
LSCALEdata reduction
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NLS

1nls


Resolution: 2.2→33.64 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 2980363.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.312 466 3.6 %RANDOM
Rwork0.279 ---
all0.281 8511 --
obs0.281 8511 66.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.035 e/Å3
Displacement parametersBiso mean: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1-9.283 Å20 Å20 Å2
2---13.968 Å20 Å2
3---4.685 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.2→33.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 2 84 1895
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
NEUTRON DIFFRACTIONc_bond_d0.0151.5
NEUTRON DIFFRACTIONc_angle_deg2.22
NEUTRON DIFFRACTIONc_dihedral_angle_d19.32
NEUTRON DIFFRACTIONc_improper_angle_d10.582.5
NEUTRON DIFFRACTIONc_mcbond_it1.341.5
NEUTRON DIFFRACTIONc_mcangle_it2.232
NEUTRON DIFFRACTIONc_scbond_it1.362
NEUTRON DIFFRACTIONc_scangle_it2.092.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 53 5.3 %
Rwork0.34 944 -
obs-997 47.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
NEUTRON DIFFRACTION1protein-H-D-planar.paramion.top
NEUTRON DIFFRACTION2ion.paramwat.top
NEUTRON DIFFRACTION3wat.paramprotein-H-D-planar.top
NEUTRON DIFFRACTION4protein-H-D-planar.param
NEUTRON DIFFRACTION5ion.param
NEUTRON DIFFRACTION6wat.param

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