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- PDB-1cnv: CRYSTAL STRUCTURE OF CONCANAVALIN B AT 1.65 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1cnv
TitleCRYSTAL STRUCTURE OF CONCANAVALIN B AT 1.65 A RESOLUTION
ComponentsCONCANAVALIN B
KeywordsSEED PROTEIN / PLANT CHITINASE / CHITIN BINDING PROTEIN
Function / homology
Function and homology information


chitinase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Chitinase Cts1-like / : / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsHennig, M.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Crystal structure of concanavalin B at 1.65 A resolution. An "inactivated" chitinase from seeds of Canavalia ensiformis.
Authors: Hennig, M. / Jansonius, J.N. / Terwisscha van Scheltinga, A.C. / Dijkstra, B.W. / Schlesier, B.
#1: Journal: To be Published
Title: Sequence Analysis of Concanavalin B from Canavalia Ensiformis Reveals Homology to Chitinases
Authors: Schlesier, B. / Nong, V.H. / Horstmann, C.H. / Hennig, M.
History
DepositionFeb 20, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 B


Theoretical massNumber of molelcules
Total (without water)33,8661
Polymers33,8661
Non-polymers00
Water5,188288
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.400, 81.400, 102.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Atom site foot note1: SER 34 - PHE 35 OMEGA = 11.26 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: PRO 56 - SER 57 OMEGA = 127.50 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: CIS PROLINE - PRO 168 / 4: CIS PROLINE - PRO 217
5: TRP 265 - ASN 266 OMEGA = 0.41 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein CONCANAVALIN B


Mass: 33866.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / Organ: SEED / Tissue: SEED / References: UniProt: P49347
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal grow
*PLUS
Method: microdialysis

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 13, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.65→15 Å / Num. obs: 40387 / % possible obs: 85.9 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.042
Reflection
*PLUS
Num. measured all: 145907 / Rmerge(I) obs: 0.0042
Reflection shell
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 1.74 Å / % possible obs: 64.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.4

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Processing

Software
NameClassification
XDSdata scaling
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing
RefinementResolution: 1.65→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.172 --
obs0.172 39989 85.8 %
Displacement parametersBiso mean: 17.8 Å2
Refinement stepCycle: LAST / Resolution: 1.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2263 0 0 288 2551
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.85
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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