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- PDB-7okr: Catalytic domain from the Aliivibrio salmonicida lytic polysaccha... -

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Basic information

Entry
Database: PDB / ID: 7okr
TitleCatalytic domain from the Aliivibrio salmonicida lytic polysaccharide monooxygenase AsLPMO10B
ComponentsChitinase B
KeywordsOXIDOREDUCTASE / LPMO / lytic polysaccharide monooxygenase / Aliivibrio salmonicida / chitinase
Function / homology
Function and homology information


chitin binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / extracellular region / metal ion binding
Similarity search - Function
N-acetylglucosamine binding protein A domain 2 / N-acetylglucosamine binding protein domain 2 / : / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Carbohydrate-binding module superfamily 5/12 / Immunoglobulin E-set
Similarity search - Domain/homology
COPPER (II) ION / DI(HYDROXYETHYL)ETHER / Chitinase B
Similarity search - Component
Biological speciesAliivibrio salmonicida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsCordara, G. / Leitl, K.D. / Loose, J.S.M. / Vaaje-Kolstad, G. / Krengel, U.
Funding support Norway, 1items
OrganizationGrant numberCountry
Norwegian Research Council249865 Norway
CitationJournal: Bmc Microbiol. / Year: 2022
Title: Chitinolytic enzymes contribute to the pathogenicity of Aliivibrio salmonicida LFI1238 in the invasive phase of cold-water vibriosis.
Authors: Skane, A. / Edvardsen, P.K. / Cordara, G. / Loose, J.S.M. / Leitl, K.D. / Krengel, U. / Sorum, H. / Askarian, F. / Vaaje-Kolstad, G.
History
DepositionMay 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Chitinase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1915
Polymers43,8091
Non-polymers3824
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-5 kcal/mol
Surface area8780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.003, 71.003, 100.203
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Chitinase B


Mass: 43809.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aliivibrio salmonicida (strain LFI1238) (bacteria)
Strain: LFI1238 / Gene: VSAL_II0217 / Production host: Escherichia coli (E. coli) / References: UniProt: B6EQJ6
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.41 Å3/Da / Density % sol: 64 % / Description: bipyramidal prism
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 0.1 M phosphate/citrate pH 4.2, 40 % PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 5, 2019 / Details: Kirkpatrick-Baez (KB) mirror pair (VFM, HFM)
RadiationMonochromator: Si (111), double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.35→33.46 Å / Num. obs: 62730 / % possible obs: 99.9 % / Redundancy: 18.2 % / CC1/2: 0.999 / Rpim(I) all: 0.022 / Χ2: 0.74 / Net I/σ(I): 15.3
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 6133 / CC1/2: 0.545 / Rpim(I) all: 0.585 / Χ2: 0.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSVERSION Mar 15, 2019 BUILT=20190806data reduction
XSCALEVERSION Mar 15, 2019 BUILT=20190806data scaling
PHASER2.8.3phasing
PHENIX1.17.1-3660refinement
Coot0.9.5model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YN2

4yn2


Resolution: 1.35→33.46 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.341 / SU ML: 0.024 / Cross valid method: FREE R-VALUE / ESU R: 0.04 / ESU R Free: 0.039
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1624 3085 4.943 %
Rwork0.1388 59329 -
all0.14 --
obs-62414 99.531 %
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: 27.772 Å2
Baniso -1Baniso -2Baniso -3
1-1.687 Å20.844 Å20 Å2
2--1.687 Å20 Å2
3----5.474 Å2
Refinement stepCycle: LAST / Resolution: 1.35→33.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 22 109 1643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131801
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181565
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.6392484
X-RAY DIFFRACTIONr_angle_other_deg1.6231.5893625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9025239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95124.112107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89415269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.646159
X-RAY DIFFRACTIONr_chiral_restr0.1030.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022443
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02451
X-RAY DIFFRACTIONr_nbd_refined0.2090.2374
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.21467
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2855
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2876
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.291
X-RAY DIFFRACTIONr_metal_ion_refined0.1110.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1020.28
X-RAY DIFFRACTIONr_nbd_other0.1350.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2230.27
X-RAY DIFFRACTIONr_mcbond_it2.7552.548890
X-RAY DIFFRACTIONr_mcbond_other2.6862.545889
X-RAY DIFFRACTIONr_mcangle_it3.1763.8521151
X-RAY DIFFRACTIONr_mcangle_other3.2053.8531152
X-RAY DIFFRACTIONr_scbond_it9.1753.078911
X-RAY DIFFRACTIONr_scbond_other9.1713.084912
X-RAY DIFFRACTIONr_scangle_it7.0924.4161333
X-RAY DIFFRACTIONr_scangle_other7.0894.4221334
X-RAY DIFFRACTIONr_lrange_it4.75431.2692050
X-RAY DIFFRACTIONr_lrange_other4.74231.1842042
X-RAY DIFFRACTIONr_rigid_bond_restr5.13133366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.3850.4132230.3814141X-RAY DIFFRACTION94.1938
1.385-1.4230.3422280.3014266X-RAY DIFFRACTION99.8667
1.423-1.4640.312100.2384164X-RAY DIFFRACTION99.9315
1.464-1.5090.2272120.194082X-RAY DIFFRACTION100
1.509-1.5590.2081820.1643899X-RAY DIFFRACTION99.9755
1.559-1.6130.1762080.1253830X-RAY DIFFRACTION99.9752
1.613-1.6740.1721830.1183643X-RAY DIFFRACTION100
1.674-1.7430.141970.1083524X-RAY DIFFRACTION100
1.743-1.820.1441680.13401X-RAY DIFFRACTION99.972
1.82-1.9090.1371450.1013243X-RAY DIFFRACTION99.9705
1.909-2.0120.1521590.1133083X-RAY DIFFRACTION100
2.012-2.1340.1391630.1132906X-RAY DIFFRACTION100
2.134-2.2810.1481740.1112705X-RAY DIFFRACTION100
2.281-2.4630.1421330.1152543X-RAY DIFFRACTION100
2.463-2.6980.1581190.1232344X-RAY DIFFRACTION100
2.698-3.0160.1461040.1412151X-RAY DIFFRACTION100
3.016-3.4810.1641070.1491868X-RAY DIFFRACTION100
3.481-4.260.136810.1411604X-RAY DIFFRACTION100
4.26-6.010.158600.1411234X-RAY DIFFRACTION100
6.01-33.4860.195290.172698X-RAY DIFFRACTION98.3762

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