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- PDB-6jms: CJP38, a beta-1,3-glucanase and allergen of Cryptomeria japonica ... -

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Basic information

Entry
Database: PDB / ID: 6jms
TitleCJP38, a beta-1,3-glucanase and allergen of Cryptomeria japonica pollen
ComponentsPollen allergen CJP38
KeywordsHYDROLASE / Beta-1 / 3-glucanase / Allergen / Tim barrel
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolases family 17 signature. / Glycoside hydrolase family 17, plant / Glycoside hydrolase family 17 / Glycosyl hydrolases family 17 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Pollen allergen CJP38
Similarity search - Component
Biological speciesCryptomeria japonica (Japanese cedar)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTakashima, T. / Numata, T. / Fukamizo, T. / Ohnuma, T.
CitationJournal: To Be Published
Title: CJP38, a beta-1,3-glucanase and allergen of Cryptomeria japonica pollen
Authors: Takashima, T. / Fukamizo, T. / Ohnuma, T. / Numata, T.
History
DepositionMar 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pollen allergen CJP38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8973
Polymers35,7731
Non-polymers1242
Water5,711317
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint7 kcal/mol
Surface area12910 Å2
Unit cell
Length a, b, c (Å)71.423, 71.423, 63.447
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Pollen allergen CJP38 / beta-1 / 3-glucanase


Mass: 35773.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptomeria japonica (Japanese cedar) / Production host: Escherichia coli (E. coli)
References: UniProt: Q588B8, glucan endo-1,3-beta-D-glucosidase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M calcium chloride, 20% Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 50705 / % possible obs: 99.4 % / Redundancy: 13.3 % / Rpim(I) all: 0.016 / Net I/σ(I): 35.5
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 2499 / CC1/2: 0.958 / Rpim(I) all: 0.116

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CYG

2cyg


Resolution: 1.5→35.711 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.944 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16821 2574 5.1 %RANDOM
Rwork0.1481 ---
obs0.14913 48087 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.541 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.22 Å2
Refinement stepCycle: 1 / Resolution: 1.5→35.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2444 0 8 317 2769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192628
X-RAY DIFFRACTIONr_bond_other_d0.0020.022396
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9563600
X-RAY DIFFRACTIONr_angle_other_deg0.96935627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0275356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.39526.102118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.41715434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.171156
X-RAY DIFFRACTIONr_chiral_restr0.0920.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212991
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02487
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_it0.6681.2071326
X-RAY DIFFRACTIONr_mcbond_other0.6431.2051325
X-RAY DIFFRACTIONr_mcangle_it1.111.8081669
X-RAY DIFFRACTIONr_mcangle_other1.1121.811670
X-RAY DIFFRACTIONr_scbond_it0.9371.3081302
X-RAY DIFFRACTIONr_scbond_other0.9321.3081302
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4561.9141916
X-RAY DIFFRACTIONr_long_range_B_refined3.31415.5373056
X-RAY DIFFRACTIONr_long_range_B_other3.20715.0973004
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.184 162 -
Rwork0.164 3548 -
obs--98.59 %
Refinement TLS params.Method: refined / Origin x: -8.4835 Å / Origin y: 24.471 Å / Origin z: -0.4226 Å
111213212223313233
T0.0053 Å2-0.0057 Å2-0 Å2-0.0112 Å2-0.0048 Å2--0.0159 Å2
L0.4075 °20.027 °20.2756 °2-0.2892 °20.0998 °2--0.213 °2
S0.0302 Å °-0.0044 Å °-0.0501 Å °-0.0119 Å °0.0109 Å °-0.009 Å °0.0141 Å °0.0047 Å °-0.0412 Å °

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