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- PDB-2baa: THE REFINED CRYSTAL STRUCTURE OF AN ENDOCHITINASE FROM HORDEUM VU... -

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Basic information

Entry
Database: PDB / ID: 2baa
TitleTHE REFINED CRYSTAL STRUCTURE OF AN ENDOCHITINASE FROM HORDEUM VULGARE L. SEEDS TO 1.8 ANGSTROMS RESOLUTION
ComponentsENDOCHITINASE (26 KD)
KeywordsHYDROLASE (O-GLYCOSYL)
Function / homology
Function and homology information


endochitinase activity / chitinase / chitin catabolic process / polysaccharide catabolic process / defense response to fungus / cell wall macromolecule catabolic 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
26 kDa endochitinase 2
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsHart, P.J. / Pfluger, H.D. / Monzingo, A.F. / Ready, M.P. / Ernst, S.R. / Hollis, T. / Robertus, J.D.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: The refined crystal structure of an endochitinase from Hordeum vulgare L. seeds at 1.8 A resolution.
Authors: Hart, P.J. / Pfluger, H.D. / Monzingo, A.F. / Hollis, T. / Robertus, J.D.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystal Structure of an Endochitinase from Hordeum Vulgare L. Seeds
Authors: Hart, P.J. / Monzingo, A.F. / Ready, M.P. / Ernst, S.R. / Robertus, J.D.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization of an Endochitinase from Hordeum Vulgare L. Seeds
Authors: Hart, P.J. / Ready, M.P. / Robertus, J.D.
#3: Journal: J.Biol.Chem. / Year: 1991
Title: Biochemical and Molecular Characterization of Three Barley Seed Proteins with Antifungal Properties
Authors: Leah, R. / Tommerup, H. / Svendsen, I. / Mundy, J.
History
DepositionJan 26, 1995Processing site: BNL
SupersessionJan 15, 1996ID: 1BAA
Revision 1.0Jan 15, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Nov 6, 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: ENDOCHITINASE (26 KD)


Theoretical massNumber of molelcules
Total (without water)25,9561
Polymers25,9561
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.500, 64.500, 43.100
Angle α, β, γ (deg.)90.00, 108.00, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO 164

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Components

#1: Protein ENDOCHITINASE (26 KD)


Mass: 25955.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 26 KD / Source: (natural) Hordeum vulgare (barley) / Organ: SEED / References: UniProt: P23951
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop / Details: microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125-30 mg/mlprotein1drop
2100 mMTris-HCl1drop
330 %satammonium sulfate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 3.88 Å / Num. obs: 18975 / % possible obs: 94 % / Num. measured all: 168007 / Rmerge(I) obs: 0.0769
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / % possible obs: 98 % / Num. unique obs: 1936 / Num. measured obs: 13313 / Rmerge(I) obs: 0.2091

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.8→5 Å / Rfactor Rwork: 0.18
Refinement stepCycle: LAST / Resolution: 1.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 0 128 1960
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg2.9
Refinement
*PLUS
Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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