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- PDB-1xqn: The 15k neutron structure of saccharide-free concanavalin A -

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Basic information

Entry
Database: PDB / ID: 1xqn
TitleThe 15k neutron structure of saccharide-free concanavalin A
ComponentsConcanavalin A
KeywordsSUGAR BINDING PROTEIN / CONCANAVALIN A / NEUTRON LAUE DIFFRACTION / BOUND D2O MOLECULES / CRYO-TEMPERATURE
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
Biological speciesCanavalia ensiformis (jack bean)
MethodNEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBlakeley, M.P. / Kalb-Gilboa, A.J. / Helliwell, J.R. / Myles, D.A.A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: The 15-K neutron structure of saccharide-free concanavalin A
Authors: Blakeley, M.P. / Kalb-Gilboa, A.J. / Helliwell, J.R. / Myles, D.A.A.
History
DepositionOct 13, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Source and taxonomy / Structure summary
Category: entity / entity_src_nat / pdbx_distant_solvent_atoms
Item: _entity.pdbx_description
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water4,089227
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)89.160, 86.129, 61.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Concanavalin 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.3 %
Description: NEUTRON DIFFRACTION HYDROGEN/DEUTERIUM EXCHANGE TECHNIQUE WAS EMPLOYED
Crystal growTemperature: 293 K / Method: batch dialysis / pH: 6.5
Details: 0.1M NaNO3, 0.05M Tris-acetate, 1mM MnCl2, 1mM CaCl2 (all in D2O), pH 6.50, BATCH DIALYSIS, temperature 293.0K

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Data collection

DiffractionMean temperature: 15 K
Diffraction sourceWavelength: 2.8-3.8
DetectorDetector: IMAGE PLATE / Date: Nov 16, 2000
RadiationMonochromator: MULTIMIRROR BANDPASS FILTER / Protocol: QUASI LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
12.81
23.81
ReflectionResolution: 2.5→32.82 Å / Num. all: 6462 / Num. obs: 6339 / % possible obs: 74.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.235 / Rsym value: 0.235 / Net I/σ(I): 5.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.3 / Num. unique all: 651 / Rsym value: 0.358 / % possible all: 54.2

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Processing

Software
NameVersionClassification
LAUEGEN/LSCALEdata collection
SCALAdata reduction
CNS1.1refinement
LAUEGEN/LSCALEdata reduction
CCP4(SCALA)data scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1.65A X-ray model of D20-grown saccharide-free concacanavalin A at 100K

100k


Resolution: 2.5→32.82 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 2949469.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.32 331 5.2 %RANDOM
Rwork0.266 ---
obs0.266 6339 74.4 %-
all-6462 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.3098 Å2 / ksol: 0.04654951 e/Å3
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1--7.8 Å20 Å20 Å2
2--12.54 Å20 Å2
3----4.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.37 Å
Luzzati d res low-6 Å
Luzzati sigma a0.7 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.5→32.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3564 0 2 561 4127
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
NEUTRON DIFFRACTIONc_bond_d0.006
NEUTRON DIFFRACTIONc_bond_d_na
NEUTRON DIFFRACTIONc_bond_d_prot
NEUTRON DIFFRACTIONc_angle_d
NEUTRON DIFFRACTIONc_angle_d_na
NEUTRON DIFFRACTIONc_angle_d_prot
NEUTRON DIFFRACTIONc_angle_deg1.6
NEUTRON DIFFRACTIONc_angle_deg_na
NEUTRON DIFFRACTIONc_angle_deg_prot
NEUTRON DIFFRACTIONc_dihedral_angle_d17.7
NEUTRON DIFFRACTIONc_dihedral_angle_d_na
NEUTRON DIFFRACTIONc_dihedral_angle_d_prot
NEUTRON DIFFRACTIONc_improper_angle_d7.31
NEUTRON DIFFRACTIONc_improper_angle_d_na
NEUTRON DIFFRACTIONc_improper_angle_d_prot
NEUTRON DIFFRACTIONc_mcbond_it1.21.5
NEUTRON DIFFRACTIONc_mcangle_it2.092
NEUTRON DIFFRACTIONc_scbond_it1.092
NEUTRON DIFFRACTIONc_scangle_it1.682.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.065 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.422 42 5.7 %
Rwork0.323 700 -
obs-700 52.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
NEUTRON DIFFRACTION1ION.PARAMION.TOP
NEUTRON DIFFRACTION2WAT.PARAMPROTEIN.TOP
NEUTRON DIFFRACTION3PROTEIN.PARAMWAT.TOP

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