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- PDB-7nm6: Crystal structure of Paradendryphiella salina PL7A alginate lyase... -

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Basic information

Entry
Database: PDB / ID: 7nm6
TitleCrystal structure of Paradendryphiella salina PL7A alginate lyase mutant Y223F in complex with di-mannuronic acid
ComponentsAlginate lyase (PL7)
KeywordsLYASE / complex / beta jelly roll / mutant / alginate lyase
Function / homologyAlginate lyase 2 / Alginate lyase / Concanavalin A-like lectin/glucanase domain superfamily / lyase activity / Alginate lyase (PL7)
Function and homology information
Biological speciesParadendryphiella salina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsFredslund, F. / Welner, D.H. / Wilkens, C.
Funding support Denmark, 1items
OrganizationGrant numberCountry
European Union (EU)9082-00021B Denmark
CitationJournal: To Be Published
Title: Crystal structure of Paradendryphiella salina PL7A alginate lyase mutant Y223F in complex with di-mannuronic acid
Authors: Fredslund, F. / Welner, D.H. / Wilkens, C.
History
DepositionFeb 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginate lyase (PL7)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0323
Polymers25,4531
Non-polymers5802
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint8 kcal/mol
Surface area9830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.280, 80.720, 81.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Alginate lyase (PL7)


Mass: 25452.715 Da / Num. of mol.: 1 / Mutation: Y22F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paradendryphiella salina (fungus) / Gene: PsAlg7A / Production host: Komagataella pastoris (fungus)
References: UniProt: A0A485PVH1, mannuronate-specific alginate lyase
#2: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 370.263 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122A-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 20% PEG 1500 and 0.1 M TBG buffer pH 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.972425 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972425 Å / Relative weight: 1
ReflectionResolution: 1.78→40.83 Å / Num. obs: 22593 / % possible obs: 97.4 % / Redundancy: 6.81 % / Biso Wilson estimate: 26.8 Å2 / CC1/2: 1 / Net I/σ(I): 11.49
Reflection shellResolution: 1.78→1.89 Å / Rmerge(I) obs: 0.73 / Num. unique obs: 3133

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
MxCuBEdata collection
XDSdata scaling
Cootmodel building
PHENIX1.18.2_3874phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NCZ

7ncz


Resolution: 1.78→40.83 Å / SU ML: 0.2307 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.1887
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1982 1129 5 %
Rwork0.1596 21454 -
obs0.1616 22583 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.07 Å2
Refinement stepCycle: LAST / Resolution: 1.78→40.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 39 216 1996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00881843
X-RAY DIFFRACTIONf_angle_d1.01082520
X-RAY DIFFRACTIONf_chiral_restr0.063301
X-RAY DIFFRACTIONf_plane_restr0.006323
X-RAY DIFFRACTIONf_dihedral_angle_d16.1282640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.860.36741180.2932252X-RAY DIFFRACTION82.61
1.86-1.960.24721370.20942597X-RAY DIFFRACTION96.51
1.96-2.080.24681430.17752706X-RAY DIFFRACTION99.93
2.08-2.240.22791420.16282704X-RAY DIFFRACTION99.96
2.24-2.460.18941430.15482732X-RAY DIFFRACTION99.93
2.46-2.820.19731440.15582741X-RAY DIFFRACTION99.97
2.82-3.550.18951480.15922806X-RAY DIFFRACTION99.97
3.55-40.830.17341540.14142916X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.218550566260.363016681697-0.2534713180612.96313811331-1.450275113174.61817857053-0.1180583484270.0660426248139-0.102197479875-0.08558939615730.0813744329534-0.2101044648040.3358074533040.1262398252770.01403424758940.1446927663750.02182287317690.002340123694940.145241728744-0.01829229710260.2235038220223.244952900311.56204574677.43268021369
21.220222616520.2313225849030.5381763972522.717142964340.2368537741352.87427918327-0.0138685660318-0.1413680126840.03572702139970.4106276258180.014664365328-0.0350412382144-0.0557778565532-0.1011498541920.00827094607210.2031030217020.0164938899327-0.01243536140940.218341176391-0.01593051920140.2221152500940.99446527059424.742649565321.7357561199
32.804172573930.600271539829-0.1670529980291.747546982810.406143168923.4261053643-0.115430135567-0.0400344099193-0.04262980881010.2628462400940.171748639825-0.07158273088130.03204999257930.0151800004386-0.01699769243710.2401795257580.00730305406667-0.05182385328030.132733839256-0.02456908172350.2545454257111.8900723115516.024620039617.4386181821
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 23 through 77 )23 - 772 - 56
22chain 'A' and (resid 78 through 223 )78 - 22357 - 211
33chain 'A' and (resid 224 through 247 )224 - 247212 - 238

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