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- PDB-3iwr: Crystal structure of class I chitinase from Oryza sativa L. japonica -

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Basic information

Entry
Database: PDB / ID: 3iwr
TitleCrystal structure of class I chitinase from Oryza sativa L. japonica
ComponentsChitinase
KeywordsHYDROLASE / class I chitinase / Oryza sativa L. japonica / Chitin-binding / Glycosidase
Function / homology
Function and homology information


chitinase activity / endochitinase activity / chitinase / chitin catabolic process / chitin binding / 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 / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. ...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 / 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 speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsKezuka, Y. / Watanabe, T. / Nonaka, T.
Citation
Journal: Proteins / Year: 2010
Title: Structure of full-length class I chitinase from rice revealed by X-ray crystallography and small-angle X-ray scattering.
Authors: Kezuka, Y. / Kojima, M. / Mizuno, R. / Suzuki, K. / Watanabe, T. / Nonaka, T.
#1: Journal: J.Biochem. / Year: 2008
Title: Role of the loop structure of the catalytic domain in rice class I chitinase
Authors: Mizuno, R. / Fukamizo, T. / Sugiyama, S. / Nishizawa, Y. / Kezuka, Y. / Nonaka, T. / Suzuki, K. / Watanabe, T.
#2: Journal: Biosci.Biotechnol.Biochem. / Year: 2008
Title: Purification and characterization of a rice class I chitinase, OsChia1b, produced in Escherichia coli
Authors: Mizuno, R. / Itoh, Y. / Nishizawa, Y. / Kezuka, Y. / Suzuki, K. / Nonaka, T. / Watanabe, T.
#3: Journal: Protein Pept.Lett. / Year: 2004
Title: Crystallization and preliminary X-ray analysis of plant class I chitinase from rice
Authors: Kezuka, Y. / Kitazaki, K. / Itoh, Y. / Watanabe, J. / Takaha, O. / Watanabe, T. / Nishizawa, Y. / Nonaka, T.
History
DepositionSep 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1.4Oct 16, 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: Chitinase
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1076
Polymers65,4802
Non-polymers6274
Water2,180121
1
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0543
Polymers32,7401
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0543
Polymers32,7401
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.082, 117.082, 77.971
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Chitinase / Endochitinase


Mass: 32740.217 Da / Num. of mol.: 2 / Fragment: Chitinase 2, residues 33-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: Cht-2, OsJ_18467 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: Q7DNA1, chitinase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 11%(w/v) PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.57→101.53 Å / Num. all: 17963 / Num. obs: 17963 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 39.187 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 10.5
Reflection shellResolution: 2.57→2.64 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1143 / Rsym value: 0.221 / % possible all: 79.4

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DKV

2dkv


Resolution: 2.57→101.53 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.887 / SU B: 8.271 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.615 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23609 967 5.1 %RANDOM
Rwork0.17858 ---
obs0.18161 17963 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.868 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0.18 Å20 Å2
2---0.36 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.57→101.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3729 0 40 121 3890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223941
X-RAY DIFFRACTIONr_bond_other_d0.0010.022726
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9265389
X-RAY DIFFRACTIONr_angle_other_deg0.942.9856527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9935498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26422.827191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28715505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3731532
X-RAY DIFFRACTIONr_chiral_restr0.290.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02896
X-RAY DIFFRACTIONr_nbd_refined0.2270.2953
X-RAY DIFFRACTIONr_nbd_other0.20.22811
X-RAY DIFFRACTIONr_nbtor_refined0.1970.21984
X-RAY DIFFRACTIONr_nbtor_other0.0890.21836
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2155
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1330.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.22
X-RAY DIFFRACTIONr_mcbond_it0.8921.53089
X-RAY DIFFRACTIONr_mcbond_other0.1281.51008
X-RAY DIFFRACTIONr_mcangle_it1.11123894
X-RAY DIFFRACTIONr_scbond_it1.53631817
X-RAY DIFFRACTIONr_scangle_it2.2174.51490
LS refinement shellResolution: 2.57→2.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 58 -
Rwork0.228 1084 -
obs--100 %

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