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- PDB-1dq0: Locked, metal-free concanavalin A, a minor species in solution -

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Basic information

Entry
Database: PDB / ID: 1dq0
TitleLocked, metal-free concanavalin A, a minor species in solution
ComponentsConcanavalin-Br
KeywordsSUGAR BINDING PROTEIN / MINOR STRUCTURAL SPECIES / SOLUTION / LOCKED STATE / DEMETALLIZED CONCANAVALIN A / BETA-SHEET
Function / homology
Function and homology information


D-mannose binding / toxin activity / metal 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 ensiformis (jack bean)
MethodX-RAY DIFFRACTION / Resolution: 1.7 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 29, 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: Version format compliance
Revision 1.3Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_nat.pdbx_beg_seq_num ..._entity.pdbx_description / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Concanavalin-Br


Theoretical massNumber of molelcules
Total (without water)25,6221
Polymers25,6221
Non-polymers00
Water3,315184
1
A: Concanavalin-Br

A: Concanavalin-Br

A: Concanavalin-Br

A: Concanavalin-Br


Theoretical massNumber of molelcules
Total (without water)102,4904
Polymers102,4904
Non-polymers00
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
Unit cell
Length a, b, c (Å)63.006, 87.290, 88.807
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-484-

HOH

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Components

#1: Protein Concanavalin-Br / Con Br / LOCKED METAL-FREE 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: P55915
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 293 K / pH: 7
Details: 2.1 M AMMONIUM SULPHATE, 120 MM SODIUM ACETATE, SOAKING OF LOCKED MNMN CON A CRYSTALS WITH THE METAL CHELATOR EDTA, pH 7.0, temperature 293.0K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117.3 mg/mlmetal-free ConA1drop
22 Mammonium sulfate1drop
360 mM1dropCH3COONa
43 %mPEG50001drop
58 mM1reservoirMnCl2
62 Mammonium sulfate1reservoir
760 mM1reservoirCH3COONa
83 %mPEG50001reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 24, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→26 Å / Num. all: 312000 / Num. obs: 311946 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.5 % / Biso Wilson estimate: 15 Å2 / Rfree details: 10 / Rmerge(I) obs: 0.061 / Net I/σ(I): 22.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 7 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 5.7 / % possible all: 99.9
Reflection
*PLUS
Num. obs: 27215 / Num. measured all: 311946
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementStarting model: 1CON

1con


Resolution: 1.7→26 Å / Cross valid method: BRUNGER / σ(F): 0 / σ(I): -3 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2721 10 %RANDOM
Rwork0.181 ---
all0.181 27215 --
obs0.181 27215 99.7 %-
Refinement stepCycle: LAST / Resolution: 1.7→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 0 185 2005
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_improper_angle_d1.7
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.312 / Rfactor Rwork: 0.301

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