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- PDB-1c57: DIRECT DETERMINATION OF THE POSITIONS OF DEUTERIUM ATOMS OF BOUND... -

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Basic information

Entry
Database: PDB / ID: 1c57
TitleDIRECT DETERMINATION OF THE POSITIONS OF DEUTERIUM ATOMS OF BOUND WATER IN CONCANAVALIN A BY NEUTRON LAUE CRYSTALLOGRAPHY
ComponentsConcanavalin-Br
KeywordsSUGAR BINDING PROTEIN / CONCANAVALIN A / NEUTRON LAUE DIFFRACTION / BOUND D2O MOLECULES
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 ...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 / NUCLEAR REACTOR / Resolution: 2.4 Å
AuthorsHabash, J. / Raftery, J. / Nuttall, R. / Price, H.J. / Lehmann, M.S. / Wilkinson, C. / Kalb, A.J. / Helliwell, J.R.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Direct determination of the positions of the deuterium atoms of the bound water in -concanavalin A by neutron Laue crystallography.
Authors: Habash, J. / Raftery, J. / Nuttall, R. / Price, H.J. / Wilkinson, C. / Kalb, 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, A.J. / Price, H. / Raftery, J. / Bradbrook, G. / Yariv, J. / Helliwell, J.R.
History
DepositionOct 26, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Database references / Structure summary
Revision 1.4Jun 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.pdbx_fragment / _entity_name_com.name
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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 / _diffrn_radiation_wavelength.wavelength / _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-Br
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7173
Polymers25,6221
Non-polymers952
Water2,666148
1
A: Concanavalin-Br
hetero molecules

A: Concanavalin-Br
hetero molecules

A: Concanavalin-Br
hetero molecules

A: Concanavalin-Br
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)89.110, 87.580, 63.260
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-Br / CONCANAVALIN A / Con Br


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: 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
Sequence detailsTHE AMINO ACID SEQUENCE IN SWS ENTRY P02866 is the pre pro concanavalin A WHICH IS POST ...THE AMINO ACID SEQUENCE IN SWS ENTRY P02866 is the pre pro concanavalin A WHICH IS POST TRANSLATIONALLY MODIFIED TO MAKE 'FINAL' CONCANAVALIN A. THERE IS A DISCREPANCY BETWEEN THE CHEMICAL SEQUENCED AND GENE SEQUENCED PROTEINS. THE DEFINITIVE SEQUENCE IS BY MIN ET AL EMBO J 1992, 11, 1103.

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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

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.31 %
Description: NEUTRON DIFFRACTION HYDROGEN/DEUTERIUM EXCHANGE TECHNIQUE WAS EMPLOYED
Crystal growpH: 6.5
Details: CRYSTALS SELECTED FOR NEUTRON STUDY WERE TRANSFERRED TO A 1ML BUFFERMADE UP OF 99.9% D2O WITH 0.1M NANO3, 0.05M TRIS-ACETATE, 1MM MNCL2 AND 1MM CACL2; PH 6.5.
Crystal grow
*PLUS
Method: batch method / Details: Greer, J., (1970) J. Mol. Biol., 48, 365.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.1 M11NaNO3
20.05 MTris-acetate11pH6.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: ILL / Beamline: LADI / Wavelength: 2.39-3.52
DetectorType: FUJI
Detector: CYLINDRICAL DETECTOR EIGHT IMAGE PLATE EACH 200X200 MM
Date: Oct 21, 1997
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
12.391
23.521
ReflectionResolution: 2.4→15.79 Å / Num. obs: 8605 / % possible obs: 89 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.222 / Rsym value: 0.222 / Net I/σ(I): 2.8
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 1.4 / % possible all: 82.2
Reflection
*PLUS
Highest resolution: 2.4 Å
Reflection shell
*PLUS
% possible obs: 82.2 % / Num. unique obs: 773 / Rmerge(I) obs: 0.436

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
INTLAUEdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.4→15.792 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.301 475 5 %RANDOM
Rwork0.27 ---
obs0.27 8605 88.5 %-
Displacement parametersBiso mean: 22.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.422 Å0.35 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 2.4→15.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 2 148 1959
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONx_bond_d0.018
NEUTRON DIFFRACTIONx_bond_d_na
NEUTRON DIFFRACTIONx_bond_d_prot
NEUTRON DIFFRACTIONx_angle_d
NEUTRON DIFFRACTIONx_angle_d_na
NEUTRON DIFFRACTIONx_angle_d_prot
NEUTRON DIFFRACTIONx_angle_deg2.2
NEUTRON DIFFRACTIONx_angle_deg_na
NEUTRON DIFFRACTIONx_angle_deg_prot
NEUTRON DIFFRACTIONx_dihedral_angle_d18.2
NEUTRON DIFFRACTIONx_dihedral_angle_d_na
NEUTRON DIFFRACTIONx_dihedral_angle_d_prot
NEUTRON DIFFRACTIONx_improper_angle_d3.7
NEUTRON DIFFRACTIONx_improper_angle_d_na
NEUTRON DIFFRACTIONx_improper_angle_d_prot
NEUTRON DIFFRACTIONx_mcbond_it
NEUTRON DIFFRACTIONx_mcangle_it
NEUTRON DIFFRACTIONx_scbond_it
NEUTRON DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.4→2.51 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.378 38 -
Rwork0.302 778 -
obs--82.5 %
Refinement
*PLUS
Rfactor obs: 0.27 / Rfactor Rfree: 0.301 / Rfactor Rwork: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg18.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg3.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.378 / Rfactor Rwork: 0.302

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