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- PDB-8bdd: Crystal structure of Bacteroides ovatus CP926 PL17 alginate lyase -

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Basic information

Entry
Database: PDB / ID: 8bdd
TitleCrystal structure of Bacteroides ovatus CP926 PL17 alginate lyase
ComponentsAlginate lyase family protein
KeywordsLYASE / (alpha/alpha)6 barrel / beta-sheet / dimer / alginate lyase
Function / homologyHeparinase II/III-like / Heparinase II/III-like protein / Alginate lyase domain / Alginate lyase / Chondroitin AC/alginate lyase / periplasmic space / lyase activity / NICKEL (II) ION / Alginate lyase family protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsRoenne, M.E. / Tandrup, T. / Wilkens, C.
Funding support Denmark, 4items
OrganizationGrant numberCountry
Danish Council for Independent Research Denmark
Novo Nordisk Foundation Denmark
The Carlsberg Foundation Denmark
Other government
CitationJournal: Appl.Environ.Microbiol. / Year: 2023
Title: Three alginate lyases provide a new gut Bacteroides ovatus isolate with the ability to grow on alginate.
Authors: Ronne, M.E. / Tandrup, T. / Madsen, M. / Hunt, C.J. / Myers, P.N. / Moll, J.M. / Holck, J. / Brix, S. / Strube, M.L. / Aachmann, F.L. / Wilkens, C. / Svensson, B.
History
DepositionOct 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alginate lyase family protein
B: Alginate lyase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,5134
Polymers165,3962
Non-polymers1172
Water13,601755
1
A: Alginate lyase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7572
Polymers82,6981
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alginate lyase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7572
Polymers82,6981
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.590, 120.950, 90.240
Angle α, β, γ (deg.)90.000, 117.760, 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 family protein


Mass: 82697.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: F3B53_17945, F3D71_17485 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5M5BZE4
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 755 / 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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium acetate, 0.1 M BIS-TRIS pH 6.5 and 25 % (w/v) polyethylene glycol 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.61→48.21 Å / Num. obs: 217247 / % possible obs: 99.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 28.27 Å2 / CC1/2: 1 / Net I/σ(I): 9.82
Reflection shellResolution: 1.61→1.67 Å / Num. unique obs: 20326 / CC1/2: 0.31

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Processing

Software
NameVersionClassification
REFMAC8refinement
PHENIX1.19.2_4158refinement
MxCuBE3data collection
XDSdata reduction
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2 model

Resolution: 1.61→48.21 Å / SU ML: 0.2559 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.2179
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2119 2276 1.05 %
Rwork0.1896 214520 -
obs0.1899 216796 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.71 Å2
Refinement stepCycle: LAST / Resolution: 1.61→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11308 0 2 755 12065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005811602
X-RAY DIFFRACTIONf_angle_d0.809615730
X-RAY DIFFRACTIONf_chiral_restr0.05231694
X-RAY DIFFRACTIONf_plane_restr0.00632030
X-RAY DIFFRACTIONf_dihedral_angle_d13.19364150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.650.41341270.442312006X-RAY DIFFRACTION89.29
1.65-1.690.36321430.342713482X-RAY DIFFRACTION100
1.69-1.730.29251440.280813482X-RAY DIFFRACTION99.99
1.73-1.770.2741420.24513460X-RAY DIFFRACTION99.99
1.77-1.830.24251430.220213461X-RAY DIFFRACTION99.99
1.83-1.890.28061430.204513473X-RAY DIFFRACTION99.99
1.89-1.950.25081430.202313498X-RAY DIFFRACTION99.99
1.95-2.030.21511430.204613475X-RAY DIFFRACTION99.99
2.03-2.120.21021440.200313483X-RAY DIFFRACTION99.95
2.12-2.240.22081420.186813469X-RAY DIFFRACTION99.96
2.24-2.380.22841440.192713518X-RAY DIFFRACTION99.94
2.38-2.560.21791430.196413493X-RAY DIFFRACTION99.96
2.56-2.820.21371440.192113530X-RAY DIFFRACTION99.96
2.82-3.220.19511430.189713517X-RAY DIFFRACTION99.92
3.22-4.060.19321440.171413552X-RAY DIFFRACTION99.91
4.06-48.210.18781440.165513621X-RAY DIFFRACTION99.41
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)
10.8610742716150.1551794869680.1368578433241.19867109893-0.5988689135540.6257144897070.0388157979085-0.075744628881-0.1632274080810.207601055557-0.0486713757021-0.00276383845399-0.0791603046266-0.0547304364952.63050967768E-50.3020884491910.00468508192316-0.0005674352245090.278610167149-0.01239276200820.249200121914-10.6838951409-18.494490040411.1714305796
20.262582369957-0.0089386955715-0.2272262599830.535980190874-0.516618897480.971937687881-0.0406133372395-0.03608078884490.05987674620050.1416937213260.04403788853230.19466874599-0.225288431087-0.1514834476532.15590228344E-60.3183170478070.038124130775-0.01179948271940.258921149549-0.04427916174710.27377566729-15.2822949374-3.431125573223.64009096759
31.29633756357-0.4678877545710.1579324989770.706319265567-0.4798331874320.278794131013-0.0546833735123-0.1163171115780.1148314445610.0360702673148-0.0487578553207-0.0684472660325-0.176372310025-0.0515735564623-3.62646945185E-50.2831521762750.01318066476490.0003873485088920.258784808571-0.02028437936250.225133608192.84888667449-4.82647545762-4.24585574352
40.8144208829340.1578298717680.3559400153640.515871479481-0.2219053768540.2984316171790.06480764330530.0979699267206-0.296346844703-0.217680378232-0.0409669793109-0.0643092943970.09137565355740.0125186891157-5.84880740414E-50.278895597050.0169004768980.01167185244370.251604125081-0.02734812178510.32599960635111.7465802014-15.7546744024-0.913748293758
50.807241507733-0.05316522097050.1474010247010.943069011768-0.006860219934761.27184537626-0.02516784774850.002974968520060.0109833890459-0.0140252805579-0.06389509290790.0341080805964-0.121013527171-0.0522738837526-2.21428370864E-50.1922922321920.0007152596780810.007684338004960.1579260568490.04017840550910.22689117424826.738401845610.33620345059.05873914882
61.13957077293-0.0952225524779-0.0927668710490.7673527989910.1782370508151.10801962702-0.05855452163810.0807952637858-0.0684942186217-0.0760884258963-0.0820895346028-0.183006010614-0.005343445576360.212048821162-0.0006876775107430.228528402393-0.003716605297660.02622612964410.2388073113090.07695790572170.30525755075438.9809267738.453590700093.23415028691
73.08427653645-0.09913730143760.2980755284670.5053267269830.03079354847820.977755440656-0.0248886893780.2643693155870.097189960062-0.08418536675170.0392876219854-0.0491527000618-0.09434683104320.145574102441-0.001914050266480.237171786208-0.0314948276376-0.01079279695550.1625117235590.008998761878310.20536115204647.7007097529-25.615090241435.3626072147
81.16804901613-0.1484222011540.3253551646681.16423895889-0.3370450324771.10307827590.00864795993218-0.109985158854-0.0475256207520.0129671399537-0.007859404249880.0625593145741-0.00813338248737-0.06574079311038.33054513235E-50.1914148265780.01855989379820.01537706627010.22986009941-0.02938566555390.18216053013417.0535255742-2.4682804625345.419998649
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 24 through 123 )AA24 - 1231 - 100
22chain 'A' and (resid 124 through 218 )AA124 - 218101 - 195
33chain 'A' and (resid 219 through 321 )AA219 - 321196 - 298
44chain 'A' and (resid 322 through 388 )AA322 - 388299 - 365
55chain 'A' and (resid 389 through 627 )AA389 - 627366 - 604
66chain 'A' and (resid 628 through 738 )AA628 - 738605 - 715
77chain 'B' and (resid 24 through 388 )BB24 - 3881 - 365
88chain 'B' and (resid 389 through 738 )BB389 - 738366 - 715

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