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- PDB-1qny: X-ray refinement of D2O soaked crystal of concanavalin A -

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Basic information

Entry
Database: PDB / ID: 1qny
TitleX-ray refinement of D2O soaked crystal of concanavalin A
ComponentsCONCANAVALIN A
KeywordsLECTIN / CONCANAVALIN A / SACCHSARIDE FREE / D2O SOAKED
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 / OTHER / Resolution: 1.8 Å
AuthorsHabash, J. / Raftery, J. / Nuttall, R. / Price, H.J. / Lehmann, M.S. / Wilkinson, C. / Kalb(Gilboa), A.J. / Helliwell, J.R.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Direct Determination of the Positions of Deuterium Atoms of Bound Water in Concanavalin a by Neutron Laue Crystallography
Authors: Habash, J. / Raftery, J. / Nuttall, R. / Price, H.J. / Lehmann, M.S. / Wilkinson, C. / Kalb(Gilboa), A.J. / Helliwell, J.R.
#1: Journal: J.Chem.Soc.,Faraday Trans. / Year: 1997
Title: Neutron Laue Diffraction Study of Concanavalin A:The Proton of Asp28
Authors: Habash, J. / Raftery, J. / Weisgerber, S. / Cassetta, A. / Lehmann, M.S. / Hoghoj, P. / Wilkinson, C. / Campbell, J.W. / Helliwell, J.R.
#2: Journal: J.Chem.Soc.,Faraday Trans. / Year: 1997
Title: The Structure of Concanavalin a and its Bound Solvent Determined with Small-Molecule Accuracy at 0.94A Resolution
Authors: Deacon, A. / Gleichmann, T. / Kalb(Gilboa), A.J. / Price, H. / Raftery, J. / Bradbrook, G. / Yariv, J. / Helliwell, J.R.
History
DepositionOct 26, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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)25,7173
Polymers25,6221
Non-polymers952
Water2,666148
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 operation3_655-x+1,y,-z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation4_565x,-y+1,-z1
MethodPQS
Unit cell
Length a, b, c (Å)89.110, 87.580, 63.260
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-2035-

HOH

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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


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.4 Å3/Da / Density % sol: 48.3 % / Description: CRYSTAL OF CONCANAVALIN A WAS SOAKED IN D2O
Crystal growpH: 6.5
Details: CRYSTALS SELECTED FOR X-RAY STUDY WERE TRANSFERRED TO A 1ML BUFFER MADE OF 99.9% D2O WITH 0.1M NANO3, 0.05M TRIS-ACETATE, 1MM MNCL2 AND 1MM CACL2 PH 6.5.
Crystal grow
*PLUS
Method: other / Details: Greer, J., (1970) J. Mol. Biol., 48, 365.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: R-AXIS II / Detector: IMAGE PLATE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→33.7 Å / Num. obs: 24110 / % possible obs: 88.1 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.248 / % possible all: 42.1
Reflection shell
*PLUS
% possible obs: 42.1 % / Num. unique obs: 1129

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: OTHER / Resolution: 1.8→33.7 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1091 5 %RANDOM
Rwork0.168 ---
obs0.168 22251 88.1 %-
Displacement parametersBiso mean: 18.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.3 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.8→33.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 2 148 1959
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.96
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.18
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
Num. reflection% reflection
Rfree95 -
Rwork1893 -
obs-57.4 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.96
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.18

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