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- PDB-6kzk: Structure of alginate lyase Aly36B mutant K143A/M171A in complex ... -

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Basic information

Entry
Database: PDB / ID: 6kzk
TitleStructure of alginate lyase Aly36B mutant K143A/M171A in complex with alginate trisaccharide
ComponentsAlginate lyase
KeywordsLYASE
Function / homology: / Polysaccharide lyase 14 / Jelly Rolls - #200 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Jelly Rolls / Sandwich / Mainly Beta / metal ion binding / Polysaccharide lyase 14 domain-containing protein
Function and homology information
Biological speciesChitinophaga sp. MD30 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.789 Å
AuthorsZhang, Y.Z. / Dong, F. / Chen, X.L.
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
DepositionSep 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 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
B: Alginate lyase
C: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2239
Polymers79,4643
Non-polymers1,7596
Water3,495194
1
A: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0743
Polymers26,4881
Non-polymers5862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area9650 Å2
MethodPISA
2
B: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0743
Polymers26,4881
Non-polymers5862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-11 kcal/mol
Surface area9660 Å2
MethodPISA
3
C: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0743
Polymers26,4881
Non-polymers5862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area9710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.770, 188.316, 91.106
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-456-

HOH

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Components

#1: Protein Alginate lyase


Mass: 26487.859 Da / Num. of mol.: 3 / Mutation: K109A, M137A
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: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 546.387 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122A-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: potassium phosphate dibasic, PEG3350

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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: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.789→50 Å / Num. obs: 21758 / % possible obs: 97.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.183 / Net I/σ(I): 15.2
Reflection shellResolution: 2.789→2.85 Å / Rmerge(I) obs: 0.395 / Num. unique obs: 1088

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.789→40.842 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2731 1018 4.68 %
Rwork0.1946 20724 -
obs0.1982 21742 94.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.64 Å2 / Biso mean: 22.7457 Å2 / Biso min: 4.29 Å2
Refinement stepCycle: final / Resolution: 2.789→40.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5625 0 114 194 5933
Biso mean--28.25 20.3 -
Num. residues----723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095892
X-RAY DIFFRACTIONf_angle_d1.3068019
X-RAY DIFFRACTIONf_chiral_restr0.083843
X-RAY DIFFRACTIONf_plane_restr0.0051038
X-RAY DIFFRACTIONf_dihedral_angle_d11.9313240
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.789-2.93550.28411320.2214237477
2.9355-3.11940.3651660.2355303899
3.1194-3.36010.31111530.2234304298
3.3601-3.69810.30581400.1922305498
3.6981-4.23270.23181230.1721300495
4.2327-5.33090.21651560.1596301095
5.3309-40.8420.25031480.2023320297

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