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- PDB-2hvm: HEVAMINE A AT 1.8 ANGSTROM RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 2hvm
TitleHEVAMINE A AT 1.8 ANGSTROM RESOLUTION
ComponentsHEVAMINE
KeywordsHYDROLASE / CHITINASE/LYSOZYME
Function / homology
Function and homology information


chitinase activity / endochitinase activity / chitinase / vacuole / chitin catabolic process / polysaccharide catabolic process / lysozyme / lysozyme activity / extracellular region
Similarity search - Function
Chitinase Cts1-like / : / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Chitinase Cts1-like / : / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsTerwisscha Van Scheltinga, A.C. / Hennig, M. / Dijkstra, B.W.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: The 1.8 A resolution structure of hevamine, a plant chitinase/lysozyme, and analysis of the conserved sequence and structure motifs of glycosyl hydrolase family 18.
Authors: Terwisscha van Scheltinga, A.C. / Hennig, M. / Dijkstra, B.W.
#1: Journal: Biochemistry / Year: 1995
Title: Stereochemistry of Chitin Hydrolysis by a Plant Chitinase/Lysozyme and X-Ray Structure of a Complex with Allosamidin. Evidence for Substrate Assisted Catalysis
Authors: Terwisscha Van Scheltinga, A.C. / Armand, S. / Kalk, K.H. / Isogai, A. / Henrissat, B. / Dijkstra, B.W.
#2: Journal: Structure / Year: 1994
Title: Crystal Structures of Hevamine, a Plant Defence Protein with Chitinase and Lysozyme Activity, and its Complex with an Inhibitor
Authors: Terwisscha Van Scheltinga, A.C. / Kalk, K.H. / Beintema, J.J. / Dijkstra, B.W.
#3: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallization of Hevamine, an Enzyme with Lysozyme/Chitinase Activity from Hevea Brasiliensis Latex
Authors: Rozeboom, H.J. / Budiani, A. / Beintema, J.J. / Dijkstra, B.W.
History
DepositionJul 2, 1996Processing site: BNL
SupersessionJan 11, 1997ID: 1HVM
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEVAMINE


Theoretical massNumber of molelcules
Total (without water)29,5731
Polymers29,5731
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.300, 57.720, 82.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HEVAMINE / CHITINASE/LYSOZYME


Mass: 29573.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hevea brasiliensis (rubber tree) / Tissue: LATEX / References: UniProt: P23472, chitinase, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.09 Å3/Da / Density % sol: 42 %
Crystal growpH: 7 / Details: pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Rozeboom, H.J., (1990) J.Mol.Biol., 212, 441. / PH range low: 9 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
135-65 %satammonium sulfate1drop
21.7-3.4 Msodium chloride1reservoirprecipitant

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Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionNum. obs: 23188 / % possible obs: 96.8 % / Observed criterion σ(I): 4 / Redundancy: 5.5 % / Rmerge(I) obs: 0.05
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 9999 Å / Num. measured all: 107989 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.85 Å / % possible obs: 80.8 % / Rmerge(I) obs: 0.149

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Processing

Software
NameClassification
MOSFLMdata reduction
TNTrefinement
RefinementResolution: 1.8→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.19 --
Rwork0.149 --
obs0.149 20520 88 %
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2087 0 0 206 2293
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0142961.3
X-RAY DIFFRACTIONt_angle_deg1.2958261.2
X-RAY DIFFRACTIONt_dihedral_angle_d22.924920
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.011022
X-RAY DIFFRACTIONt_gen_planes0.036280
X-RAY DIFFRACTIONt_it2.68214860
X-RAY DIFFRACTIONt_nbd0.015740
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg22.90
X-RAY DIFFRACTIONt_planar_d0.012
X-RAY DIFFRACTIONt_plane_restr0.030

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