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

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Basic information

Entry
Database: PDB / ID: 8bjr
TitleCrystal structure of Paradendryphiella salina PL7C alginate lyase
ComponentsAlginate lyase
KeywordsLYASE / beta-jelly roll / alginate lyase
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: 1.1 Å
AuthorsFredslund, F. / Welner, D.H. / Wilkens, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Paradendryphiella salina PL7C alginate lyase
Authors: Fredslund, F. / Welner, D.H. / Wilkens, C.
History
DepositionNov 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: 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)25,8324
Polymers25,5441
Non-polymers2883
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-34 kcal/mol
Surface area9790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.791, 39.804, 42.527
Angle α, β, γ (deg.)73.630, 76.353, 70.072
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Alginate lyase


Mass: 25544.244 Da / Num. of mol.: 1
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M (NH4)2SO4; 25% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.6888 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 1.1→27.5 Å / Num. obs: 72994 / % possible obs: 90.09 % / Redundancy: 3.8 % / Biso Wilson estimate: 9.01 Å2 / CC1/2: 1 / Net I/σ(I): 7.41
Reflection shellResolution: 1.1→1.14 Å / Num. unique obs: 7116 / CC1/2: 0.83

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Processing

Software
NameVersionClassification
MxCuBE3data collection
PHENIX1.19.2_4158refinement
autoPROCdata processing
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YWF

6ywf


Resolution: 1.1→27.5 Å / SU ML: 0.0688 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 15.1139
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1499 3666 5.02 %
Rwork0.1265 69328 -
obs0.1277 72994 90.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.33 Å2
Refinement stepCycle: LAST / Resolution: 1.1→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 15 397 2170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571914
X-RAY DIFFRACTIONf_angle_d0.92162633
X-RAY DIFFRACTIONf_chiral_restr0.0827295
X-RAY DIFFRACTIONf_plane_restr0.0085346
X-RAY DIFFRACTIONf_dihedral_angle_d13.7269693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.21621250.19932608X-RAY DIFFRACTION88.79
1.11-1.130.22881480.19812622X-RAY DIFFRACTION88.7
1.13-1.140.20521340.1862607X-RAY DIFFRACTION88.53
1.14-1.160.21231380.17752639X-RAY DIFFRACTION88.75
1.16-1.180.20621430.17052678X-RAY DIFFRACTION89.3
1.18-1.20.19251660.16532542X-RAY DIFFRACTION88.47
1.2-1.220.19241160.16622705X-RAY DIFFRACTION89.64
1.22-1.240.17041380.15832603X-RAY DIFFRACTION88.48
1.24-1.260.18071400.14962611X-RAY DIFFRACTION88.37
1.26-1.290.2171210.14872708X-RAY DIFFRACTION88.85
1.29-1.320.18571110.14442612X-RAY DIFFRACTION88.78
1.32-1.350.16341320.14262705X-RAY DIFFRACTION91.49
1.35-1.380.15281470.13152720X-RAY DIFFRACTION92.13
1.38-1.420.15791530.12422743X-RAY DIFFRACTION91.27
1.42-1.460.14471170.12142726X-RAY DIFFRACTION91.95
1.46-1.510.16281420.1142697X-RAY DIFFRACTION91.46
1.51-1.560.15861390.11032666X-RAY DIFFRACTION90.86
1.56-1.620.13171430.10562712X-RAY DIFFRACTION91.18
1.62-1.70.12561580.10832722X-RAY DIFFRACTION91.28
1.7-1.790.15711670.1122647X-RAY DIFFRACTION90.83
1.79-1.90.14151440.10732638X-RAY DIFFRACTION89.45
1.9-2.050.13081670.10442630X-RAY DIFFRACTION89.79
2.05-2.250.12761370.10752667X-RAY DIFFRACTION89.3
2.25-2.580.13951370.11412680X-RAY DIFFRACTION91.17
2.58-3.250.13141560.11582774X-RAY DIFFRACTION93.76
3.25-27.50.13751470.13252666X-RAY DIFFRACTION90.02

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