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- PDB-6ywf: Crystal structure of Paradendryphiella salina PL7A alginate lyase -

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Basic information

Entry
Database: PDB / ID: 6ywf
TitleCrystal structure of Paradendryphiella salina PL7A alginate lyase
ComponentsAlginate lyase (PL7)
KeywordsLYASE / Alginate lyase / fungal / polysaccharide lyase family 7 / PL7
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: 1.9 Å
AuthorsWilkens, C. / Fredslund, F. / Welner, D.H.
CitationJournal: To Be Published
Title: Crystal structure of Paradendryphiella salina PL7A alginate lyase
Authors: Wilkens, C. / Fredslund, F. / Welner, D.H.
History
DepositionApr 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginate lyase (PL7)


Theoretical massNumber of molelcules
Total (without water)25,4691
Polymers25,4691
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.768, 80.442, 81.375
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) / Variant (production host): X-33 / References: UniProt: A0A485PVH1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 20% PEG 1500, 0.1 M TBG buffer

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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: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→40.22 Å / Num. obs: 18624 / % possible obs: 98.32 % / Redundancy: 8.5 % / Biso Wilson estimate: 17.72 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07987 / Rpim(I) all: 0.02868 / Rrim(I) all: 0.08505 / Net I/σ(I): 17.26
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 4.94 / Num. unique obs: 11623 / CC1/2: 0.947 / CC star: 0.986 / Rpim(I) all: 0.1418 / Rrim(I) all: 0.3682 / % possible all: 93.09

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CWS

2cws


Resolution: 1.9→40.22 Å / SU ML: 0.1473 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.3243
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1878 1830 9.96 %
Rwork0.1507 16542 -
obs0.1545 18372 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.56 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 0 237 1968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311769
X-RAY DIFFRACTIONf_angle_d0.70542416
X-RAY DIFFRACTIONf_chiral_restr0.0496287
X-RAY DIFFRACTIONf_plane_restr0.0033313
X-RAY DIFFRACTIONf_dihedral_angle_d15.3529619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.22221310.17781186X-RAY DIFFRACTION92.94
1.95-2.010.24941350.17681210X-RAY DIFFRACTION95.73
2.01-2.070.19961300.15931231X-RAY DIFFRACTION97.01
2.07-2.150.19351350.15371256X-RAY DIFFRACTION98.1
2.15-2.230.21011340.151251X-RAY DIFFRACTION98.37
2.23-2.340.19751440.14691272X-RAY DIFFRACTION98.81
2.34-2.460.18681370.14381260X-RAY DIFFRACTION99.01
2.46-2.610.18041440.14591277X-RAY DIFFRACTION99.58
2.61-2.810.17821410.15411279X-RAY DIFFRACTION99.58
2.81-3.10.20311510.15861288X-RAY DIFFRACTION99.65
3.1-3.540.20041450.15671308X-RAY DIFFRACTION99.86
3.55-4.460.16641470.12921328X-RAY DIFFRACTION100
4.47-40.220.16021560.15211396X-RAY DIFFRACTION99.49
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)
13.88954953242-0.105876678388-0.03901687435673.50266791323-0.8746335383452.76670915799-0.08585584900530.007962223295490.0946000113294-0.1634060694290.0415181594454-0.1133270670130.1487687923730.1836571904940.02716982668460.1028925660860.02060786549480.0164886844980.103000672346-0.01599096790680.07948504331564.1210820303713.20675956125.04708140962
20.7868164129780.1235737727920.1691379627461.46937095896-0.3458916303111.32060105142-0.016464975884-0.03795364997430.03003899815090.0575228330989-0.00222816781653-0.06731943892120.01845478523180.0612462268430.02872430797980.100706344803-0.0002612906885420.004091530795540.132997453363-0.002176133356270.1378089410933.2305312173819.326953854117.4171637448
31.812341350761.53285598835-0.02336533724311.457598237570.2232809283.708141395860.13025658393-0.4494563605860.02382282010640.771044496282-0.127833874737-0.03254016003570.131845201926-0.07371711574770.006010289834440.2740213783920.0122213962631-0.006519807096460.190232011349-0.01461369185960.1301681397312.219658323822.34405517433.5314312006
46.949664468715.72733034692-0.7905201008549.10729999413-1.804588716924.091713785820.20363039549-0.3888587756780.3148300158580.710764004955-0.185129429424-0.01764302378-0.3138592533780.109404898012-0.004075544461010.1472385523660.0586583190177-0.02352310902640.137009767236-0.02390290675340.1324504371914.2202685950529.324455044628.964483443
51.547261255721.49842228432-0.1559400682262.01903205071-0.6101830166761.14219735449-0.0517550050064-0.07750769141290.0391384272278-0.1224416613470.206989431820.474105025310.186307327264-0.187642546392-0.1720580249940.174451104749-0.01797930786420.01746633821210.182033503870.0002081419564640.17343071997-7.3548230712618.569878335321.7077434317
63.234261292232.27444260047-0.9527225156665.05773404521-0.755921693083.36394164960.185737161098-0.2421806122510.3345520435160.331162496833-0.2418998183220.566179846273-0.313338157543-0.257724800432-0.008321600221330.1578153478760.02299308816620.02245072280140.169837332449-0.02790492584920.226958838534-8.1289951554729.626923145224.5405296493
70.156899923483-0.209493524558-0.05562184231441.113046981340.4280326233041.474945815020.0025253918015-0.0913289845160.09586739216540.124133249483-0.0015564518242-0.26900629983-0.1542230581150.03922849389370.02318440072430.118429812708-0.00769278862093-0.004118622916490.121514225312-0.003149766440020.1717671047244.8704420840728.483342098217.3181302656
82.032517426410.815046595265-0.3162733305472.21837114677-0.1765249527842.63278508456-0.0773112285775-0.133012245884-0.00994510183348-0.0740964947260.1479484014390.0992156591244-0.0692676656724-0.194588194321-0.003638453782660.134775636369-0.009077107993660.006025977762120.0779789925876-0.03076782751130.1069418553981.4285915855615.604559992316.8426013461
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 63 )23 - 631 - 41
22chain 'A' and (resid 64 through 147 )64 - 14742 - 127
33chain 'A' and (resid 148 through 161 )148 - 161128 - 141
44chain 'A' and (resid 162 through 176 )162 - 176142 - 156
55chain 'A' and (resid 177 through 189 )177 - 189157 - 169
66chain 'A' and (resid 190 through 208 )190 - 208170 - 188
77chain 'A' and (resid 209 through 225 )209 - 225189 - 205
88chain 'A' and (resid 226 through 247 )226 - 247206 - 227

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