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

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Basic information

Entry
Database: PDB / ID: 7oof
TitleCrystal structure of Paradendryphiella salina PL7A alginate lyase in complex with tri-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 / alpha-D-mannopyranuronic acid / Alginate lyase (PL7)
Function and homology information
Biological speciesParadendryphiella salina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 in complex with tri-mannuronic acid
Authors: Fredslund, F. / Welner, D.H. / Wilkens, C.
History
DepositionMay 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alginate lyase (PL7)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4034
Polymers25,4691
Non-polymers9353
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint15 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.810, 81.110, 80.690
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: 25468.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paradendryphiella salina (fungus) / Gene: PsAlg7A / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A485PVH1
#2: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 546.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122A-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-MAV / alpha-D-mannopyranuronic acid / alpha-D-mannuronic acid / D-mannuronic acid / mannuronic acid


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O7 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranuronic acidCOMMON NAMEGMML 1.0
a-D-ManpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManASNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.24 Å3/Da / Density % sol: 45 %
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: 0.953798 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953798 Å / Relative weight: 1
ReflectionResolution: 1.3→40.34 Å / Num. obs: 56932 / % possible obs: 99.3 % / Redundancy: 12.53 % / Biso Wilson estimate: 16.88 Å2 / CC1/2: 1 / Net I/σ(I): 18.42
Reflection shellResolution: 1.3→1.38 Å / Num. unique obs: 8735 / CC1/2: 0.46 / % possible all: 95.7

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
Cootmodel building
PHASERphasing
PHENIX1.19refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NCZ

7ncz


Resolution: 1.3→40.34 Å / SU ML: 0.1656 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.1991
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1737 2101 3.69 %
Rwork0.1585 54826 -
obs0.159 56927 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.81 Å2
Refinement stepCycle: LAST / Resolution: 1.3→40.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 63 250 2055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711913
X-RAY DIFFRACTIONf_angle_d0.99772619
X-RAY DIFFRACTIONf_chiral_restr0.0865317
X-RAY DIFFRACTIONf_plane_restr0.0065337
X-RAY DIFFRACTIONf_dihedral_angle_d18.5924659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.33371270.36393306X-RAY DIFFRACTION91.52
1.33-1.360.35481360.32983561X-RAY DIFFRACTION98.12
1.36-1.40.3051400.28063640X-RAY DIFFRACTION99.87
1.4-1.440.23181390.22593629X-RAY DIFFRACTION100
1.44-1.490.18481380.19613618X-RAY DIFFRACTION100
1.49-1.540.18961400.16783634X-RAY DIFFRACTION99.97
1.54-1.60.19491390.17243646X-RAY DIFFRACTION100
1.6-1.670.19761410.17593668X-RAY DIFFRACTION100
1.67-1.760.18111410.15743685X-RAY DIFFRACTION100
1.76-1.870.17811400.14513645X-RAY DIFFRACTION100
1.87-2.020.17561410.14053683X-RAY DIFFRACTION100
2.02-2.220.1561410.14083690X-RAY DIFFRACTION99.97
2.22-2.540.14491430.13953733X-RAY DIFFRACTION99.97
2.54-3.20.17051440.15073748X-RAY DIFFRACTION100
3.2-40.340.15371510.14693940X-RAY DIFFRACTION99.93
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)
14.25552818090.4846198442090.1182558743862.85218346111-0.6383938520462.50809023738-0.0548981403069-0.03443802498930.04676790939120.1836464107180.001316780156230.229683399266-0.142507471768-0.1348340036610.03953690720610.1181456311750.009238649986320.01823537712540.088554414999-0.01498803745550.105646727162-13.110100775315.26972214087.48819095204
20.7716334781310.2200939065240.1788167711711.182423290420.02424640843071.02177102776-0.005767756496080.0129099801638-0.03178568932460.019302871096-0.01859898335640.05559473611140.0366558379889-0.04807519627370.0214756944370.103496602467-0.009671532190690.003478308158180.130191696243-0.0003215630403740.122902854707-11.96553786432.852313477841.25626862474
31.045854439240.2342050501390.2242544118581.17326420830.06098492978962.125517636-0.0007608417373450.0973277434326-0.156805438946-0.07890303275810.0178796489966-0.117683462430.1810618773610.07438599629-0.01729056530710.138187786527-0.00602908237960.008665930407460.13319704993-0.01454835599880.146990427003-7.13633594673-4.39843277032-6.39715666191
41.04621495428-0.3099619859720.7147301008841.739896618310.1933025645571.66021968996-0.06965127251280.00579020253264-0.0775418867189-0.0364827048468-0.0124363028502-0.123571784425-0.08865096272530.06612868434350.07568735900890.140619826782-0.0125158326368-0.001765931050070.137889133205-0.009800055360050.0984107398351-10.45980332553.3009678234.65687729248
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 0 through 63 )0 - 631 - 42
22chain 'A' and (resid 64 through 147 )64 - 14743 - 126
33chain 'A' and (resid 148 through 223 )148 - 223127 - 202
44chain 'A' and (resid 224 through 247 )224 - 247203 - 226

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