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- PDB-5k2l: Crystal structure of LysM domain from Volvox carteri chitinase -

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Basic information

Entry
Database: PDB / ID: 5k2l
TitleCrystal structure of LysM domain from Volvox carteri chitinase
ComponentsChitinase, lysozyme
KeywordsHYDROLASE / chitin binding module / chitinase / Volvox carteri / green alga
Function / homology
Function and homology information


Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesVolvox carteri f. nagariensis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKitaoku, Y. / Numata, T. / Fukamizo, T. / Ohnuma, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Strategic Project to Support the Formation of Research Bases at Private Universities: Matching Fund Subsidy from the MEXTS1101035 Japan
CitationJournal: Plant Mol. Biol. / Year: 2017
Title: Chitin oligosaccharide binding to the lysin motif of a novel type of chitinase from the multicellular green alga, Volvox carteri.
Authors: Kitaoku, Y. / Fukamizo, T. / Numata, T. / Ohnuma, T.
History
DepositionMay 19, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 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, lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3522
Polymers5,2901
Non-polymers621
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.130, 29.130, 94.257
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein/peptide Chitinase, lysozyme


Mass: 5290.043 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 104-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Volvox carteri f. nagariensis (plant) / Gene: chi4, VOLCADRAFT_127242 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle(DE3) / References: UniProt: D8UFB5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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 Å3/Da / Density % sol: 34.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium citrate tribasic dihydrate, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 13481 / % possible obs: 99.5 % / Redundancy: 23.5 % / Net I/σ(I): 73
Reflection shellResolution: 1.2→1.22 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PXV

4pxv


Resolution: 1.2→27.83 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.063 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.043 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17959 688 5.1 %RANDOM
Rwork0.13871 ---
obs0.14073 12739 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 9.587 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.2 Å2
Refinement stepCycle: 1 / Resolution: 1.2→27.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms369 0 4 89 462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.02419
X-RAY DIFFRACTIONr_bond_other_d0.0010.02413
X-RAY DIFFRACTIONr_angle_refined_deg1.9991.939577
X-RAY DIFFRACTIONr_angle_other_deg2.8523.006940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.578557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.65523.520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.041567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.457155
X-RAY DIFFRACTIONr_chiral_restr0.1360.266
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021493
X-RAY DIFFRACTIONr_gen_planes_other0.020.02104
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_it1.420.752207
X-RAY DIFFRACTIONr_mcbond_other1.1630.743205
X-RAY DIFFRACTIONr_mcangle_it1.4081.124259
X-RAY DIFFRACTIONr_mcangle_other1.5821.13260
X-RAY DIFFRACTIONr_scbond_it3.041.13212
X-RAY DIFFRACTIONr_scbond_other3.0351.137213
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3621.559314
X-RAY DIFFRACTIONr_long_range_B_refined3.9039.916590
X-RAY DIFFRACTIONr_long_range_B_other3.99.933591
X-RAY DIFFRACTIONr_rigid_bond_restr8.8583832
X-RAY DIFFRACTIONr_sphericity_free14.86656
X-RAY DIFFRACTIONr_sphericity_bonded6.9635903
LS refinement shellResolution: 1.201→1.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.164 50 -
Rwork0.127 919 -
obs--98.88 %

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