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- PDB-7c8g: Structure of alginate lyase AlyC3 -

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Basic information

Entry
Database: PDB / ID: 7c8g
TitleStructure of alginate lyase AlyC3
ComponentsAlginate lyase AlyC3
KeywordsLYASE / alginate / alginate lyase
Function / homologyJelly Rolls - #200 / Jelly Rolls / Sandwich / Mainly Beta / SUCCINIC ACID
Function and homology information
Biological speciesPsychromonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.1 Å
AuthorsZhang, Y.Z. / Xu, F. / Chen, X.L. / Wang, P.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural and molecular basis for the substrate positioning mechanism of a new PL7 subfamily alginate lyase from the arctic.
Authors: Xu, F. / Chen, X.L. / Sun, X.H. / Dong, F. / Li, C.Y. / Li, P.Y. / Ding, H. / Chen, Y. / Zhang, Y.Z. / Wang, P.
History
DepositionMay 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginate lyase AlyC3
B: Alginate lyase AlyC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8196
Polymers60,3982
Non-polymers4204
Water6,828379
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.902, 45.603, 305.876
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alginate lyase AlyC3


Mass: 30199.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychromonas sp. (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) polyethylene glycol (PEG) 3350 and 0.2 M succinic acid (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 38033 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 31.8
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.41 / Num. unique obs: 3711

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
PHASERphasing
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→41.629 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2733 1880 4.99 %
Rwork0.2047 35776 -
obs0.2081 37656 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.81 Å2 / Biso mean: 35.5263 Å2 / Biso min: 18.49 Å2
Refinement stepCycle: final / Resolution: 2.1→41.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4256 0 28 379 4663
Biso mean--38.35 38.07 -
Num. residues----528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074374
X-RAY DIFFRACTIONf_angle_d0.9145888
X-RAY DIFFRACTIONf_chiral_restr0.056620
X-RAY DIFFRACTIONf_plane_restr0.005768
X-RAY DIFFRACTIONf_dihedral_angle_d13.8162618
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.15640.32111160.2486265896
2.1564-2.21990.35211580.2453266599
2.2199-2.29150.31051240.23992762100
2.2915-2.37340.3451240.2352274599
2.3734-2.46840.30941570.22982681100
2.4684-2.58070.30781310.23442745100
2.5807-2.71680.28021590.23442724100
2.7168-2.88690.33471680.2417272299
2.8869-3.10980.30521470.2338270799
3.1098-3.42260.27251510.2118278599
3.4226-3.91750.25711400.1893277999
3.9175-4.93440.24311480.1556281898
4.9344-41.6290.1991570.1778298599

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