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- PDB-3aqu: Crystal structure of a class V chitinase from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 3aqu
TitleCrystal structure of a class V chitinase from Arabidopsis thaliana
ComponentsAt4g19810
KeywordsHYDROLASE / stress response / TIM barrel / chitin
Function / homology
Function and homology information


exo-chitinase (non-reducing end) / exochitinase activity / secretory vesicle / response to jasmonic acid / chitinase activity / response to abscisic acid / endochitinase activity / chitinase / chitin catabolic process / chitin binding ...exo-chitinase (non-reducing end) / exochitinase activity / secretory vesicle / response to jasmonic acid / chitinase activity / response to abscisic acid / endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / response to salt stress
Similarity search - Function
Chitinase A; domain 3 - #10 / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases ...Chitinase A; domain 3 - #10 / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Class V chitinase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsNumata, T. / Ohnuma, T. / Osawa, T. / Fukamizo, T.
CitationJournal: Planta / Year: 2011
Title: A class V chitinase from Arabidopsis thaliana: gene responses, enzymatic properties, and crystallographic analysis
Authors: Ohnuma, T. / Numata, T. / Osawa, T. / Mizuhara, M. / Lampela, O. / Juffer, A.H. / Skriver, K. / Fukamizo, T.
History
DepositionNov 19, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: At4g19810
B: At4g19810
C: At4g19810
D: At4g19810
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,2637
Polymers154,6954
Non-polymers5673
Water10,467581
1
A: At4g19810
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0523
Polymers38,6741
Non-polymers3782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: At4g19810
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8632
Polymers38,6741
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: At4g19810


Theoretical massNumber of molelcules
Total (without water)38,6741
Polymers38,6741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: At4g19810


Theoretical massNumber of molelcules
Total (without water)38,6741
Polymers38,6741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.574, 75.079, 97.347
Angle α, β, γ (deg.)73.63, 73.34, 68.47
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
At4g19810 / A class V chitinase from Arabidopsis thaliana / AtChiC / Putative chitinase


Mass: 38673.824 Da / Num. of mol.: 4 / Fragment: residues in UNP 25-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT4g19810 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: O81862, chitinase
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 3.08 Å3/Da / Density % sol: 60.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 100mM trisodium citrate, 20% PEG10000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 17, 2010 / Details: mirrors
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 116512 / % possible obs: 94.5 % / Redundancy: 2.9 % / Rsym value: 0.102 / Net I/σ(I): 7.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 1.9 / % possible all: 88.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ALF

3alf


Resolution: 2.01→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.898 / SU B: 3.869 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22715 5800 5 %RANDOM
Rwork0.19626 ---
obs0.1978 110709 94.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.842 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å2-0.28 Å20.66 Å2
2---0.25 Å20.11 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.01→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10564 0 39 581 11184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02210912
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.92714915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63551372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66723.051472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.318151508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1171560
X-RAY DIFFRACTIONr_chiral_restr0.0770.21599
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218560
X-RAY DIFFRACTIONr_mcbond_it0.5321.56838
X-RAY DIFFRACTIONr_mcangle_it1210963
X-RAY DIFFRACTIONr_scbond_it1.42534074
X-RAY DIFFRACTIONr_scangle_it2.3294.53952
LS refinement shellResolution: 2.005→2.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 361 -
Rwork0.271 7421 -
obs--85.62 %

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