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- PDB-6kcw: Structure of alginate lyase Aly36B -

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Basic information

Entry
Database: PDB / ID: 6kcw
TitleStructure of alginate lyase Aly36B
ComponentsAlginate lyase
KeywordsLYASE / Alginate lyase
Function / homology: / Polysaccharide lyase 14 / Prokaryotic membrane lipoprotein lipid attachment site profile. / PHOSPHATE ION / Uncharacterized protein
Function and homology information
Biological speciesChitinophaga sp. MD30 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å
AuthorsDong, F. / Chen, X.L. / Zhang, Y.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31870052 China
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Alginate Lyase Aly36B is a New Bacterial Member of the Polysaccharide Lyase Family 36 and Catalyzes by a Novel Mechanism With Lysine as Both the Catalytic Base and Catalytic Acid.
Authors: Dong, F. / Xu, F. / Chen, X.L. / Li, P.Y. / Li, C.Y. / Li, F.C. / Chen, Y. / Wang, P. / Zhang, Y.Z.
History
DepositionJun 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1223
Polymers26,9871
Non-polymers1352
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-20 kcal/mol
Surface area9640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.770, 89.492, 46.856
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-454-

HOH

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Components

#1: Protein Alginate lyase


Mass: 26986.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chitinophaga sp. MD30 (bacteria) / Gene: CK934_20815 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A249T061
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: potassium phosphate monobasic/ sodium phosphate dibasic, polyethylene glycol (PEG) 8,000, and sodium chloride.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.28→46.86 Å / Num. obs: 10564 / % possible obs: 98.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 25.06
Reflection shellResolution: 2.28→2.38 Å / Num. unique obs: 1026

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.28→46.86 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.41
RfactorNum. reflection% reflection
Rfree0.235 511 4.87 %
Rwork0.195 --
obs0.197 10500 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.55 Å2 / Biso mean: 43.1462 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.28→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 6 73 1988
Biso mean--48.68 40.65 -
Num. residues----244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2817-2.51130.33941220.241234994
2.5113-2.87460.29721370.2388249399
2.8746-3.62150.23191270.2031251398
3.6215-46.860.19191250.1674263498

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