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- PDB-2z39: Crystal structure of Brassica juncea chitinase catalytic module G... -

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Basic information

Entry
Database: PDB / ID: 2z39
TitleCrystal structure of Brassica juncea chitinase catalytic module Glu234Ala mutant (Bjchi3-E234A)
ComponentsChitinase
KeywordsHYDROLASE / chitinase / endochitinase / family 19 / conformational changes
Function / homology
Function and homology information


defense response to other organism / chitinase activity / chitin catabolic process / chitin binding / 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: 1.7 Å
AuthorsUbhayasekera, W. / 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 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,07421
Polymers54,4012
Non-polymers67419
Water7,584421
1
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4849
Polymers27,2001
Non-polymers2848
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,59012
Polymers27,2001
Non-polymers39011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.988, 47.254, 77.668
Angle α, β, γ (deg.)90.000, 100.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chitinase


Mass: 27200.404 Da / Num. of mol.: 2 / Fragment: catalytic module, UNP residues 146-389 / Mutation: E234A
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: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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 Å3/Da / Density % sol: 36.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 20% PEG 3350, 0.2M ammonium formate, pH 6.6, 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: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionRedundancy: 3.6 % / Av σ(I) over netI: 2.3 / Number: 169437 / Rmerge(I) obs: 0.21 / Rsym value: 0.21 / D res high: 1.7 Å / D res low: 76.472 Å / Num. obs: 47339 / % possible obs: 97.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
1.71.7997.510.5430.5432.6
5.3876.9298.710.0970.0975.5
3.85.3899.410.1160.1166
3.13.899.610.1850.1856.1
2.693.19910.3270.3275.2
2.42.6996.410.4110.4113.8
2.192.495.810.4270.4273
2.032.1996.110.1490.1492.7
1.92.0396.710.230.232.6
1.791.997.210.3450.3452.6
ReflectionResolution: 1.7→76.472 Å / Num. obs: 47339 / % possible obs: 97.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.21 / Rsym value: 0.21 / Net I/σ(I): 2.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 1.2 / Num. measured all: 17883 / Num. unique all: 6889 / Rsym value: 0.543 / % possible all: 97.5

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation1.82 Å35.07 Å
Translation1.82 Å35.07 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z37

2z37


Resolution: 1.7→37.1 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.352 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2311 5.1 %RANDOM
Rwork0.178 ---
obs0.18 45609 94.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.965 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.74 Å2
2---0.11 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3825 0 19 421 4265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223956
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.9295387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0875500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95824.127189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6815585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6061518
X-RAY DIFFRACTIONr_chiral_restr0.0980.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023157
X-RAY DIFFRACTIONr_nbd_refined0.2060.21914
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22752
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2319
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.215
X-RAY DIFFRACTIONr_mcbond_it0.8931.52497
X-RAY DIFFRACTIONr_mcangle_it1.46523921
X-RAY DIFFRACTIONr_scbond_it2.21631706
X-RAY DIFFRACTIONr_scangle_it3.4124.51460
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 198 -
Rwork0.224 3219 -
obs-3417 96.85 %

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