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- PDB-1dxj: Structure of the chitinase from jack bean -

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Basic information

Entry
Database: PDB / ID: 1dxj
TitleStructure of the chitinase from jack bean
ComponentsCLASS II CHITINASE
KeywordsHYDROLASE / FAMILY 19 GLYCOSIDASE / ALPHA HELICAL PROTEIN
Function / homology
Function and homology information


chitinase activity / chitin catabolic process / chitin binding / defense response to fungus / cell wall macromolecule catabolic process / carbohydrate metabolic process
Similarity search - Function
Chitinases family 19 signature 1. / Endochitinase; domain 2 / Endochitinase, domain 2 / Chitinases family 19 signature 2. / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily ...Chitinases family 19 signature 1. / Endochitinase; domain 2 / Endochitinase, domain 2 / Chitinases family 19 signature 2. / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesCANAVALIA ENSIFORMIS (jack bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHahn, M. / Hennig, M. / Schlesier, B. / Hohne, W.
Citation
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Refined Structure of the Chitinase from Barley Seeds at 2.0 A Resolution
Authors: Song, S.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystal Structure of an Endochitinase from Hordeum Vulgare L. Seeds
Authors: Hartmonzingoready, E.J.
History
DepositionJan 10, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CLASS II CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2352
Polymers26,1391
Non-polymers961
Water2,810156
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.690, 67.690, 110.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein CLASS II CHITINASE


Mass: 26139.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) CANAVALIA ENSIFORMIS (jack bean) / Organ: SEED / References: UniProt: O81934, chitinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 55.89 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 9.5
Details: PROTEIN CONCENTRATION: 15 MG/ML PROTEIN BUFFER: 0.1 M TRIS, PH 9.5, PRECIPITANT: 1.6 M AMMONIUM SULFATE MIXING EQUAL VOLUMES IN SITTING DROPS, AT ROOM TEMPERATURE
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
20.1 MTris1droppH9.5
31.6 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: ENRAF NONIUS FR591 / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→12.3 Å / Num. obs: 24446 / % possible obs: 92.2 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rsym value: 0.059 / Net I/σ(I): 9.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.268 / % possible all: 84.6
Reflection
*PLUS
Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 84.6 % / Rmerge(I) obs: 0.268

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
XDSdata reduction
XDSdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CNS

1cns


Resolution: 1.8→12.3 Å / Isotropic thermal model: RESTRAINED / Cross valid method: ALL, EXCEPT FINAL CYCLES / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2410 9.1 %RANDOM
Rwork0.182 ---
obs0.182 24446 92.2 %-
Displacement parametersBiso mean: 16.2 Å2
Refinement stepCycle: LAST / Resolution: 1.8→12.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 5 156 2003
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.449
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.41
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.443
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 / % reflection obs: 84.6 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.41
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.443

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