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- PDB-1dq6: Manganese;Manganese concanavalin A at pH 7.0 -

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Basic information

Entry
Database: PDB / ID: 1dq6
TitleManganese;Manganese concanavalin A at pH 7.0
ComponentsConcanavalin-A
KeywordsSUGAR BINDING PROTEIN / concanavalin A / lectin / metal binding / manganese / binuclear
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 ...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)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsBouckaert, J. / Dewallef, Y. / Poortmans, F. / Wyns, L. / Loris, R.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: The structural features of concanavalin A governing non-proline peptide isomerization
Authors: Bouckaert, J. / Dewallef, Y. / Poortmans, F. / Wyns, L. / Loris, R.
History
DepositionDec 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 14, 2017Group: Database references / Refinement description ...Database references / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_nat / software / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _software.name / _struct_ref_seq.ref_id
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.6Feb 7, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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

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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)25,7323
Polymers25,6221
Non-polymers1102
Water2,252125
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)102,92912
Polymers102,4904
Non-polymers4408
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_546x,-y-1,-z+11
Buried area10190 Å2
ΔGint-83 kcal/mol
Surface area33250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.200, 87.410, 89.300
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-427-

HOH

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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.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2 M ammonium sulphate, 60 mM sodium acetate at pH 7, 3% PEGMe 5000, 1 mM MnCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jul 28, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→8 Å / Num. all: 19671 / Num. obs: 19671 / % possible obs: 87.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.53
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 7.69 / Num. unique all: 2196 / % possible all: 77.7

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Processing

Software
NameVersionClassification
MADNESSdata collection
ROTAVATAdata reduction
AMoREphasing
X-PLOR3.843refinement
MADNESSdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 1.9→8 Å / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.186 --
all0.186 16969 -
obs0.186 16969 89 %
Displacement parametersBiso mean: 14.35 Å2
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 2 125 1936
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg2.9
X-RAY DIFFRACTIONx_dihedral_angle_d27.5
X-RAY DIFFRACTIONx_improper_angle_d1.7
LS refinement shellResolution: 1.9→2 Å / Total num. of bins used: 10 /
Rfactor% reflection
Rwork0.233 -
obs-77.7 %

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