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- PDB-7xmh: Crystal structure of a rice class IIIb chitinase, Oschib2 -

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Basic information

Entry
Database: PDB / ID: 7xmh
TitleCrystal structure of a rice class IIIb chitinase, Oschib2
ComponentsPutative class III chitinase
KeywordsHYDROLASE / GH18 chitinase / family 8 pathogenesis-related protein
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Chitinase-like / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / Putative class III chitinase
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsJun, T. / Tomoya, T. / Tomoyuki, N. / Takayuki, O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plant Sci. / Year: 2023
Title: Characterization of two rice GH18 chitinases belonging to family 8 of plant pathogenesis-related proteins.
Authors: Tanaka, J. / Takashima, T. / Abe, N. / Fukamizo, T. / Numata, T. / Ohnuma, T.
History
DepositionApr 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative class III chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4918
Polymers32,0631
Non-polymers4287
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-1 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.698, 69.403, 73.019
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative class III chitinase


Mass: 32062.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: OSJNBa0061K21.7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8S870
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Sodium acetate trihydrate pH 4.5, 3.0 M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.18→46.72 Å / Num. obs: 101845 / % possible obs: 99.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 32.49
Reflection shellResolution: 1.18→1.2 Å / Rmerge(I) obs: 0.167 / Num. unique obs: 4567

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RL3

4rl3


Resolution: 1.18→46.72 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.374 / SU ML: 0.018 / Cross valid method: NONE / ESU R: 0.033 / ESU R Free: 0.033
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1658 5083 4.995 %
Rwork0.1597 96673 -
all0.16 --
obs-101756 99.848 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 9.561 Å2
Baniso -1Baniso -2Baniso -3
1-0.399 Å20 Å20 Å2
2---0.057 Å20 Å2
3----0.342 Å2
Refinement stepCycle: LAST / Resolution: 1.18→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2213 0 28 335 2576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132311
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172041
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.6393148
X-RAY DIFFRACTIONr_angle_other_deg1.5661.5684728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.625293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77723.304115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.10215317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.197158
X-RAY DIFFRACTIONr_chiral_restr0.0750.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022660
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02504
X-RAY DIFFRACTIONr_nbd_refined0.2060.2467
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.21930
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21161
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2988
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2182
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0020.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2520.217
X-RAY DIFFRACTIONr_nbd_other0.2150.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2020.226
X-RAY DIFFRACTIONr_mcbond_it0.7550.8891162
X-RAY DIFFRACTIONr_mcbond_other0.7470.8881159
X-RAY DIFFRACTIONr_mcangle_it1.241.3341448
X-RAY DIFFRACTIONr_mcangle_other1.2411.3341449
X-RAY DIFFRACTIONr_scbond_it1.0120.9661149
X-RAY DIFFRACTIONr_scbond_other1.0110.9671150
X-RAY DIFFRACTIONr_scangle_it1.531.4121697
X-RAY DIFFRACTIONr_scangle_other1.531.4121698
X-RAY DIFFRACTIONr_lrange_it3.13411.6372679
X-RAY DIFFRACTIONr_lrange_other2.88110.9962612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.210.1633570.1596975X-RAY DIFFRACTION98.0607
1.21-1.2440.1593650.1616883X-RAY DIFFRACTION100
1.244-1.280.1593720.1576687X-RAY DIFFRACTION100
1.28-1.3190.1753610.1566524X-RAY DIFFRACTION100
1.319-1.3620.163090.1516344X-RAY DIFFRACTION100
1.362-1.410.1573230.1476131X-RAY DIFFRACTION100
1.41-1.4630.1622710.1535969X-RAY DIFFRACTION100
1.463-1.5230.1493220.1455683X-RAY DIFFRACTION100
1.523-1.590.1523080.1435462X-RAY DIFFRACTION100
1.59-1.6680.1412860.1425228X-RAY DIFFRACTION100
1.668-1.7580.1622860.1494961X-RAY DIFFRACTION100
1.758-1.8650.1462310.1474773X-RAY DIFFRACTION100
1.865-1.9930.1452520.1484430X-RAY DIFFRACTION100
1.993-2.1530.1782000.1484189X-RAY DIFFRACTION100
2.153-2.3580.1641810.1513865X-RAY DIFFRACTION99.9753
2.358-2.6350.1761790.1643506X-RAY DIFFRACTION99.9729
2.635-3.0410.1721490.183114X-RAY DIFFRACTION100
3.041-3.7220.2021370.1722640X-RAY DIFFRACTION100
3.722-5.2490.1561320.1712081X-RAY DIFFRACTION100

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