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- PDB-9irq: Alginate lyase (Microbulbifer sp. ALW1) -

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Basic information

Entry
Database: PDB / ID: 9irq
TitleAlginate lyase (Microbulbifer sp. ALW1)
ComponentsAlginate lyase AlgL17
KeywordsHYDROLASE / Exooligoalginatelyase / Cloning / Biochemical characterization / Microbulbifer
Function / homologymannuronate-specific alginate lyase / poly(beta-D-mannuronate) lyase activity / Alginate lyase domain / Alginate lyase / Heparinase II/III-like / Heparinase II/III-like, C-terminal / Chondroitin AC/alginate lyase / periplasmic space / Alginate lyase AlgL17
Function and homology information
Biological speciesMicrobulbifer sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsZhu, Y.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)No. 22178142 China
CitationJournal: To Be Published
Title: Molecular cloning and characterization of AlgL17, a new exo-oligoalginate lyase from Microbulbifer sp. ALW1
Authors: Zhu, Y.B.
History
DepositionJul 16, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginate lyase AlgL17
B: Alginate lyase AlgL17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,5914
Polymers157,4602
Non-polymers1312
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-90 kcal/mol
Surface area48540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.108, 90.421, 88.287
Angle α, β, γ (deg.)90.00, 110.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alginate lyase AlgL17


Mass: 78729.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbulbifer sp. (strain ALW1) (bacteria)
Gene: algl17 / Production host: Escherichia phage EcSzw-2 (virus)
References: UniProt: A0A3Q8CBV3, mannuronate-specific alginate lyase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.07 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Glycine ,PEG 4000, Glycine,PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 29, 2022 / Details: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.98→82.96 Å / Num. obs: 84249 / % possible obs: 94.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.5
Reflection shellResolution: 1.98→2.09 Å / Rmerge(I) obs: 0.525 / Num. unique obs: 11039

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Processing

Software
NameVersionClassification
PHENIX1.12refinement
XDS1data reduction
XDS1data scaling
PHENIX1.12phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4nei

4nei


Resolution: 1.98→82.96 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2391 4003 -
Rwork0.188 --
obs-84135 94.51 %
Refinement stepCycle: LAST / Resolution: 1.98→82.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11086 0 2 376 11464
LS refinement shellResolution: 1.9843→2.0552 Å
RfactorNum. reflection% reflection
Rfree0.3195 429 -
Rwork0.2552 --
obs-8808 99.17 %

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