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- PDB-8qli: Crystal structure of Paradendryphiella salina PL7C alginate lyase... -

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Basic information

Entry
Database: PDB / ID: 8qli
TitleCrystal structure of Paradendryphiella salina PL7C alginate lyase mutant H124 soaked with with tetra-mannuronic acid
ComponentsAlginate lyase
KeywordsLYASE / alginate lyase / beta jelly-roll / complex
Function / homologyAlginate lyase 2 / Alginate lyase / Concanavalin A-like lectin/glucanase domain superfamily / lyase activity / Alginate lyase
Function and homology information
Biological speciesParadendryphiella salina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsWilkens, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant H124 soaked with with tetra-mannuronic acid
Authors: Wilkens, C.
History
DepositionSep 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2432
Polymers25,5201
Non-polymers7231
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint10 kcal/mol
Surface area9420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.540, 38.770, 75.170
Angle α, β, γ (deg.)90.000, 116.910, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-626-

HOH

21A-645-

HOH

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Components

#1: Protein Alginate lyase


Mass: 25520.199 Da / Num. of mol.: 1 / Mutation: H124N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paradendryphiella salina (fungus) / Gene: PsAlg7C / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A7I9C8Z1
#2: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid- ...beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 722.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a1122A-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 1.97 Å3/Da / Density % sol: 37.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 30% PEG3350, 0.1M Bis-Tris pH 5.5, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.12→38.67 Å / Num. obs: 75488 / % possible obs: 98.33 % / Redundancy: 5.4 % / Biso Wilson estimate: 7.65 Å2 / CC1/2: 0.78 / Net I/σ(I): 12.98
Reflection shellResolution: 1.12→1.15 Å / Num. unique obs: 4449 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
PHENIXdev_4788refinement
MxCuBE3data collection
XDSdata reduction
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→38.67 Å / SU ML: 0.0703 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.0434
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1678 2099 2.78 %
Rwork0.1439 73389 -
obs0.1445 75488 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.02 Å2
Refinement stepCycle: LAST / Resolution: 1.12→38.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 49 419 2196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00682003
X-RAY DIFFRACTIONf_angle_d1.0792764
X-RAY DIFFRACTIONf_chiral_restr0.092321
X-RAY DIFFRACTIONf_plane_restr0.0086362
X-RAY DIFFRACTIONf_dihedral_angle_d13.1418733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.150.20281240.1754321X-RAY DIFFRACTION86.66
1.15-1.170.17921330.16264694X-RAY DIFFRACTION94.72
1.17-1.210.161370.15874780X-RAY DIFFRACTION97.19
1.21-1.240.18921390.16024858X-RAY DIFFRACTION98.33
1.24-1.280.1961400.1634906X-RAY DIFFRACTION99.16
1.28-1.330.18951410.15384916X-RAY DIFFRACTION99.68
1.33-1.380.17911420.15294957X-RAY DIFFRACTION99.96
1.38-1.440.17041420.14934980X-RAY DIFFRACTION100
1.44-1.520.15651410.1474942X-RAY DIFFRACTION99.92
1.52-1.620.17261430.14434996X-RAY DIFFRACTION99.96
1.62-1.740.14581430.13944974X-RAY DIFFRACTION99.98
1.74-1.910.15241410.13774931X-RAY DIFFRACTION99.8
1.91-2.190.16391430.13495007X-RAY DIFFRACTION99.83
2.19-2.760.17291430.13995022X-RAY DIFFRACTION99.79
2.76-38.670.16291470.13615105X-RAY DIFFRACTION99.62

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