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- PDB-3cql: Crystal Structure of GH family 19 chitinase from Carica papaya -

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Basic information

Entry
Database: PDB / ID: 3cql
TitleCrystal Structure of GH family 19 chitinase from Carica papaya
ComponentsEndochitinase
KeywordsHYDROLASE / GLYCOSYL HYDROLASE / CHITINASE / N-ACETYL-D-GLUCOSAMINE / Carbohydrate metabolism / Chitin degradation / Chitin-binding / Glycosidase / Polysaccharide degradation / Vacuole
Function / homology
Function and homology information


chitinase / chitinase activity / vacuole / chitin catabolic process / chitin binding / polysaccharide catabolic process / defense response / cell wall macromolecule catabolic process
Similarity search - Function
Chitinases family 19 signature 1. / Chitinases family 19 signature 2. / Endochitinase; domain 2 / Endochitinase, domain 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. / Chitinases family 19 signature 2. / Endochitinase; domain 2 / Endochitinase, domain 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
2-acetamido-2-deoxy-alpha-D-glucopyranose / Endochitinase
Similarity search - Component
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsHuet, J. / Rucktoa, P. / Clantin, B. / Azarkan, M. / Looze, Y. / Villeret, V. / Wintjens, R.
Citation
Journal: Biochemistry / Year: 2008
Title: X-ray Structure of Papaya Chitinase Reveals the Substrate Binding Mode of Glycosyl Hydrolase Family 19 Chitinases.
Authors: Huet, J. / Rucktooa, P. / Clantin, B. / Azarkan, M. / Looze, Y. / Villeret, V. / Wintjens, R.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Crystallization and preliminary X-ray analysis of a family 19 glycosyl hydrolase from Carica papaya latex.
Authors: Huet, J. / Azarkan, M. / Looze, Y. / Villeret, V. / Wintjens, R.
#2: Journal: Cell.Mol.Life Sci. / Year: 2006
Title: Structural characterization of two papaya chitinases, a family GH19 of glycosyl hydrolases.
Authors: Huet, J. / Wyckmans, J. / Wintjens, R. / Boussard, P. / Raussens, V. / Vandenbussche, G. / Ruysschaert, J.M. / Azarkan, M. / Looze, Y.
History
DepositionApr 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endochitinase
B: Endochitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,94213
Polymers53,1382
Non-polymers1,80411
Water7,044391
1
A: Endochitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4216
Polymers26,5691
Non-polymers8525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endochitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5217
Polymers26,5691
Non-polymers9526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.000, 44.490, 76.810
Angle α, β, γ (deg.)90.00, 94.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Endochitinase


Mass: 26568.998 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: latex / Source: (natural) Carica papaya (papaya) / References: UniProt: P85084, chitinase

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Sugars , 2 types, 6 molecules

#2: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 396 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsACCORDING TO THE AUTHORS THE SEQUENCE DETERMINATION FOR UNP P85084 WAS DONE BY MASS SPECTROSCOPY ...ACCORDING TO THE AUTHORS THE SEQUENCE DETERMINATION FOR UNP P85084 WAS DONE BY MASS SPECTROSCOPY AND WITH THE TECHNIQUE THE DISTINCTION BETWEEN LEU AND ILE COULD NOT BE MADE

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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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: lithium sulfate 0.17M, PEG 4000 25%, glycerol 15%, N-acetyl-D-glucosamine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.978872
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978872 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 71589 / Rmerge(I) obs: 0.064
Reflection shellResolution: 1.5→1.59 Å / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 0.064

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å19.68 Å
Translation3 Å19.68 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→19.68 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.08 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18679 3596 5 %RANDOM
Rwork0.16096 ---
obs0.16226 67987 95.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.551 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3744 0 116 391 4251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223989
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9785429
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9765486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26722.558172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89615554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5151530
X-RAY DIFFRACTIONr_chiral_restr0.0750.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023126
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.22107
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22746
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2321
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6241.52464
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01123878
X-RAY DIFFRACTIONr_scbond_it1.57631759
X-RAY DIFFRACTIONr_scangle_it2.4134.51550
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 253 -
Rwork0.198 4846 -
obs--93.54 %

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