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- PDB-2z37: Crystal structure of Brassica juncea chitinase catalytic module (... -

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Basic information

Entry
Database: PDB / ID: 2z37
TitleCrystal structure of Brassica juncea chitinase catalytic module (Bjchi3)
ComponentsChitinase
KeywordsHYDROLASE / chitinase / endochitinase / family 19 / conformational changes
Function / homology
Function and homology information


chitinase activity / chitin catabolic process / chitin binding / defense response to fungus / cell wall macromolecule catabolic process
Similarity search - Function
Chitinases family 19 signature 2. / Endochitinase; domain 2 / Endochitinase, domain 2 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain ...Chitinases family 19 signature 2. / Endochitinase; domain 2 / Endochitinase, domain 2 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesBrassica juncea (brown mustard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsUbhayasekera, W. / Berglund, G. / Bergfors, T. / Mowbray, S.L.
CitationJournal: Febs J. / Year: 2007
Title: Crystal structures of a family 19 chitinase from Brassica juncea show flexibility of binding cleft loops
Authors: Ubhayasekera, W. / Tang, C.M. / Ho, S.W.T. / Berglund, G. / Bergfors, T. / Chye, M.-L. / Mowbray, S.L.
History
DepositionJun 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitinase
B: Chitinase
C: Chitinase
D: Chitinase


Theoretical massNumber of molelcules
Total (without water)108,2174
Polymers108,2174
Non-polymers00
Water13,295738
1
A: Chitinase


Theoretical massNumber of molelcules
Total (without water)27,0541
Polymers27,0541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitinase


Theoretical massNumber of molelcules
Total (without water)27,0541
Polymers27,0541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chitinase


Theoretical massNumber of molelcules
Total (without water)27,0541
Polymers27,0541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Chitinase


Theoretical massNumber of molelcules
Total (without water)27,0541
Polymers27,0541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.249, 61.821, 75.359
Angle α, β, γ (deg.)79.340, 89.520, 88.900
Int Tables number1
Space group name H-MP1
Detailsbiological unit is the catalytic module with two chitin binding modules

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Components

#1: Protein
Chitinase


Mass: 27054.215 Da / Num. of mol.: 4 / Fragment: catalytic module, UNP residues 146-389
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica juncea (brown mustard) / Gene: Bjchi1 / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): KM71 / References: UniProt: Q9SQF7, chitinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 738 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 40.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 10% mono methyl PEG 5000, 0.2M unbuffered sodium acetate, 0.1M sodium acetate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionRedundancy: 2 % / Av σ(I) over netI: 20.7 / Number: 265499 / Rmerge(I) obs: 0.145 / Χ2: 1.02 / D res high: 1.53 Å / D res low: 50 Å / Num. obs: 130887 / % possible obs: 95.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
1.531.5693.110.2480.9891.6
4.155099.210.1461.0353.3
3.34.1598.910.1641.113.6
2.883.398.310.1641.0213.2
2.622.8896.710.0760.9581.8
2.432.6296.810.0831.051.8
2.292.4396.410.0831.0631.8
2.172.2996.110.0921.0411.8
2.082.179610.0831.0211.8
22.0895.610.0941.021.8
1.93295.710.0951.1271.8
1.871.9394.910.1380.9771.8
1.811.8795.510.1070.9731.8
1.771.8195.310.1141.0131.8
1.721.779510.1250.9371.8
1.681.7294.810.1440.8971.8
1.651.6894.610.15711.8
1.621.6594.710.1630.9671.8
1.581.6294.410.1811.0171.8
1.561.589510.2160.9261.9
ReflectionResolution: 1.53→50 Å / Num. obs: 130887 / % possible obs: 95.8 % / Redundancy: 2 % / Rmerge(I) obs: 0.145 / Χ2: 1.02 / Net I/σ(I): 20.7
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.248 / Num. unique all: 6382 / Χ2: 0.989 / % possible all: 93.1

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2 Å43.21 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model of Brassica juncea chitinase built on PDB ENTRY 2BAA

2baa


Resolution: 1.53→42.23 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.878 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 7824 6 %RANDOM
Rwork0.185 ---
obs0.188 130862 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.145 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0.12 Å2-0.1 Å2
2---0.31 Å20.48 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.53→42.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7664 0 0 738 8402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227927
X-RAY DIFFRACTIONr_angle_refined_deg1.1341.93110800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.84351000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37924.173381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.334151188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9441537
X-RAY DIFFRACTIONr_chiral_restr0.0870.21079
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026313
X-RAY DIFFRACTIONr_nbd_refined0.1990.23773
X-RAY DIFFRACTIONr_nbtor_refined0.3150.25470
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2583
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.220
X-RAY DIFFRACTIONr_mcbond_it1.0721.54972
X-RAY DIFFRACTIONr_mcangle_it1.67427841
X-RAY DIFFRACTIONr_scbond_it2.57733438
X-RAY DIFFRACTIONr_scangle_it3.634.52941
LS refinement shellResolution: 1.531→1.571 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 542 -
Rwork0.147 8595 -
obs-9137 100 %

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