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- PDB-5h7t: A GH19 chitinase domain from the Cryptomeria japnonica pollen (CJ... -

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Basic information

Entry
Database: PDB / ID: 5h7t
TitleA GH19 chitinase domain from the Cryptomeria japnonica pollen (CJP-4) allergen
ComponentsClass IV chitinase
KeywordsHYDROLASE / Cryptomeria japonica / GH19 Chitinase / CJP-4 / Allergen
Function / homology
Function and homology information


endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / defense response to fungus / cell wall macromolecule catabolic process / killing of cells of another organism / extracellular region
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 / Chitin-binding, type 1, conserved site / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. ...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 / Chitin-binding, type 1, conserved site / 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 speciesCryptomeria japonica (Japanese cedar)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsTakashima, T. / Umemoto, N. / Numata, T. / Ohnuma, T. / Fukamizo, T.
CitationJournal: To Be Published
Title: Crystal structure of GH19 catalytic domain of CJP-4 allergen from Japanese cedar (Cryptomeria japonica) pollen.
Authors: Takashima, T. / Umemoto, N. / Numata, T. / Ohnuma, T. / Fukamizo, T.
History
DepositionNov 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Class IV chitinase


Theoretical massNumber of molelcules
Total (without water)22,6331
Polymers22,6331
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.011, 74.304, 35.811
Angle α, β, γ (deg.)90.00, 99.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Class IV chitinase


Mass: 22632.629 Da / Num. of mol.: 1 / Fragment: UNP residues 77-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptomeria japonica (Japanese cedar) / Gene: cjp-4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5NTA4, chitinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 1.91 Å3/Da / Density % sol: 35.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M BIS-TRIS pH 6.5 15 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.19→37.15 Å / Num. obs: 51012 / % possible obs: 94.08 % / Redundancy: 7.3 % / Net I/σ(I): 20.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→37.15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.415 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.039 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16375 2590 5.1 %RANDOM
Rwork0.14643 ---
obs0.14733 48394 94.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 7.646 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0 Å20.03 Å2
2--0.17 Å20 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 1.19→37.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1524 0 0 183 1707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0191651
X-RAY DIFFRACTIONr_bond_other_d0.0010.021398
X-RAY DIFFRACTIONr_angle_refined_deg2.0011.8972264
X-RAY DIFFRACTIONr_angle_other_deg1.03833222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5625228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9225.12878
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.17815224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.698154
X-RAY DIFFRACTIONr_chiral_restr0.1570.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022078
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02436
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8710.634876
X-RAY DIFFRACTIONr_mcbond_other0.870.633875
X-RAY DIFFRACTIONr_mcangle_it1.2320.9561113
X-RAY DIFFRACTIONr_mcangle_other1.2320.9561114
X-RAY DIFFRACTIONr_scbond_it1.7090.742775
X-RAY DIFFRACTIONr_scbond_other1.710.741774
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4321.0671150
X-RAY DIFFRACTIONr_long_range_B_refined3.6196.062150
X-RAY DIFFRACTIONr_long_range_B_other3.4335.6542071
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.192→1.223 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.166 179 -
Rwork0.157 3414 -
obs--89.85 %

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