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

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Basic information

Entry
Database: PDB / ID: 8qiz
TitleCrystal structure of Paradendryphiella salina PL7C alginate lyase mutant H124N soaked with with penta-mannuronic acid
ComponentsAlginate lyase
KeywordsLYASE / Beta-jelly roll / alginate lyase / 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: 1.13 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 penta-mannuronic acid
Authors: Wilkens, C.
History
DepositionSep 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3173
Polymers25,5201
Non-polymers1,7972
Water6,071337
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint27 kcal/mol
Surface area9370 Å2
Unit cell
Length a, b, c (Å)42.690, 69.360, 42.920
Angle α, β, γ (deg.)90.000, 114.640, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 1074.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-4LGulpAa1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a1122A-1b_1-5][a1121A-1a_1-5]/1-2-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][a-L-GulpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}}}}}LINUCSPDB-CARE
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 273 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: Jun 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.13→39.01 Å / Num. obs: 162684 / % possible obs: 96.94 % / Redundancy: 6 % / Biso Wilson estimate: 13.38 Å2 / CC1/2: 1 / Net I/σ(I): 11.57
Reflection shellResolution: 1.13→1.16 Å / Num. unique obs: 4929 / CC1/2: 0.62

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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: 1.13→39.01 Å / SU ML: 0.1377 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 18.0889
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1585 2102 1.29 %
Rwork0.1264 160581 -
obs0.1268 162683 96.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.67 Å2
Refinement stepCycle: LAST / Resolution: 1.13→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1745 0 122 337 2204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622000
X-RAY DIFFRACTIONf_angle_d1.04382751
X-RAY DIFFRACTIONf_chiral_restr0.0877341
X-RAY DIFFRACTIONf_plane_restr0.0085349
X-RAY DIFFRACTIONf_dihedral_angle_d13.4045683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.160.32221270.33659537X-RAY DIFFRACTION86.21
1.16-1.180.33731340.293610239X-RAY DIFFRACTION92.78
1.18-1.220.23231390.2410512X-RAY DIFFRACTION95.06
1.22-1.250.26721350.205110557X-RAY DIFFRACTION95.88
1.25-1.290.15991400.175610784X-RAY DIFFRACTION97.34
1.29-1.340.16711400.163310788X-RAY DIFFRACTION97.93
1.34-1.390.20611400.148510898X-RAY DIFFRACTION98.77
1.39-1.460.16521420.134310899X-RAY DIFFRACTION98.96
1.46-1.530.12541450.106311067X-RAY DIFFRACTION99.04
1.53-1.630.13341440.098810900X-RAY DIFFRACTION99.28
1.63-1.750.13351440.099210936X-RAY DIFFRACTION99.61
1.75-1.930.1371450.113510987X-RAY DIFFRACTION98.95
1.93-2.210.12851410.109810864X-RAY DIFFRACTION98.41
2.21-2.790.14261410.119110783X-RAY DIFFRACTION97.82
2.79-39.010.16491450.113810830X-RAY DIFFRACTION97.92

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