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- PDB-8bdq: Crystal structure of Bacteroides ovatus CP926 PL38 alginate lyase -

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Basic information

Entry
Database: PDB / ID: 8bdq
TitleCrystal structure of Bacteroides ovatus CP926 PL38 alginate lyase
ComponentsAlginate lyase family protein
KeywordsLYASE / (alpha/alpha)7 barrel / tetramer / alginate lyase
Function / homology
Function and homology information


periplasmic space / lyase activity
Similarity search - Function
Alginate lyase domain / Alginate lyase / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Alginate lyase family protein
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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 Denmark
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
C: Alginate lyase family protein
D: Alginate lyase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,3699
Polymers183,8894
Non-polymers4805
Water1,44180
1
A: Alginate lyase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0682
Polymers45,9721
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alginate lyase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1643
Polymers45,9721
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alginate lyase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0682
Polymers45,9721
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alginate lyase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0682
Polymers45,9721
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)196.700, 88.090, 144.000
Angle α, β, γ (deg.)90.000, 120.060, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Alginate lyase family protein


Mass: 45972.230 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: F3B53_17925, F3D71_22350 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5M5BWR5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.94 Å3/Da / Density % sol: 58.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium sulfate, 0.1 M BIS-TRIS pH 5.5 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: 0.976254 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: 0.976254 Å / Relative weight: 1
ReflectionResolution: 2.11→49.17 Å / Num. obs: 121042 / % possible obs: 99 % / Redundancy: 3.89 % / Biso Wilson estimate: 48.91 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.5
Reflection shellResolution: 2.11→2.24 Å / Num. unique obs: 19034 / CC1/2: 0.53

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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

Resolution: 2.11→48.12 Å / SU ML: 0.4139 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.6931
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2811 2100 1.74 %
Rwork0.2551 118858 -
obs0.2555 120958 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.97 Å2
Refinement stepCycle: LAST / Resolution: 2.11→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12207 0 25 80 12312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002712588
X-RAY DIFFRACTIONf_angle_d0.564617070
X-RAY DIFFRACTIONf_chiral_restr0.03871801
X-RAY DIFFRACTIONf_plane_restr0.00462186
X-RAY DIFFRACTIONf_dihedral_angle_d13.96114728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.160.39951310.38957381X-RAY DIFFRACTION92.96
2.16-2.220.33661400.34967926X-RAY DIFFRACTION99.83
2.22-2.280.32821400.32967898X-RAY DIFFRACTION99.84
2.28-2.340.38291410.31837977X-RAY DIFFRACTION99.89
2.34-2.420.36251400.31497957X-RAY DIFFRACTION99.96
2.42-2.50.37261410.31887964X-RAY DIFFRACTION99.95
2.5-2.60.37091400.32557945X-RAY DIFFRACTION99.98
2.61-2.720.36511410.30137965X-RAY DIFFRACTION99.89
2.72-2.870.31541410.28527995X-RAY DIFFRACTION99.82
2.87-3.050.30881410.28377957X-RAY DIFFRACTION99.75
3.05-3.280.3331400.28717967X-RAY DIFFRACTION99.25
3.28-3.610.28111390.24737913X-RAY DIFFRACTION99.25
3.61-4.130.24081410.22137961X-RAY DIFFRACTION98.96
4.13-5.210.19451410.20147975X-RAY DIFFRACTION98.93
5.21-48.120.24981430.22288077X-RAY DIFFRACTION98.42
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)
10.6275311147660.3980232228490.4273434580341.31017238649-0.00964955007780.732508050873-0.1311169458530.02618242242990.0805103027631-0.02615946323340.03734655147490.0571017056392-0.01386014292470.3274024388882.13359354289E-50.4084593506820.0524497451936-0.01002515262930.517374091240.05283425368930.418609597286-57.477136087965.148512598569.8639724201
20.670224671661-0.227569836072-0.5695894887940.245036536530.4514741641150.8697691828420.103552393248-0.167756968016-0.199551433018-0.1061973089670.0347052634756-0.007903998666470.2152379329520.158434335895-4.69913043511E-50.422096313495-0.0193082421155-0.1094571163520.318895609519-0.04770076081330.530579758666-25.255068137233.01313889518.30960741102
30.31152362895-0.246246748030.3850380282831.16399663527-0.3817074858550.3654969584960.0146300713733-0.1843926229340.012341890846-0.03087646166970.141186253790.209238513350.0424966912077-0.0812402987962-1.45938903931E-50.422010152749-0.0725742890378-0.0391701139460.391914704139-0.04447632632530.482160139665-38.896046666141.42631068988.81459507464
40.2756050089660.02746748409670.5275300122330.857020817688-0.02465372032820.8486161510480.0602220197784-0.111392381388-0.0164496893598-0.0754964022818-0.0002386176838810.0289035912029-0.1524677785980.0837160866859-4.52369268012E-50.342611230967-0.0936992757486-0.002165208254290.380995471467-0.06986718151150.370586012478-29.152252561451.715687860612.8939186092
50.354100721576-0.5775735181120.1280009943490.8214509974660.2408129963690.5874303421980.16239589387-0.3852108232820.02877698272610.2072591804320.0005131226495960.1922660456820.057945544863-0.01189312285450.0006792698106170.420990114045-0.12453353146-0.08550816443280.572015498169-0.01248628188270.442819930383-28.058418487138.64521908429.2875081871
61.118058203270.8976348676030.2697731814790.762601012185-0.3346258681280.8546295565750.170916572976-0.1110578109050.1163891671630.142954264375-0.1719069830380.336565381453-0.153098623259-0.1066117675448.39730528811E-50.4998600518680.02443348829030.1026896415450.3945267154550.06148556706010.488653258984-73.889634814240.30572907246.83182788957
70.0300286807266-0.0644598264502-0.03385602499660.3211915565980.2796779358560.1725886768560.18263143811-0.0204233382793-0.131623057644-0.00870153958669-0.182141036291-0.4723760828860.213956894950.222363473836-3.61443263067E-50.519808317363-0.0526415467075-0.003051161002280.6036421150180.1289218981570.67690717048-46.561450937525.454440421713.236421154
80.5679087955410.2273424513150.6608977344960.58759788578-0.08404910110670.5011068661010.08312585111180.02530653363490.0871640649462-0.028367911385-0.0906050826717-0.0728952024137-0.06142557044370.02920573370635.56180795621E-50.4710474487470.03029507043360.05917678882360.4567265661330.07582067744220.484574865876-68.93099055231.2101498463.6911107459
90.2743362249630.135113396687-0.4913181331121.212137187410.1389912382460.6888820966680.163171449541-0.09089664067980.2771055675010.101242564299-0.270469960029-0.007531585156720.05725738997670.1094066011850.000376240311630.51716517981-0.05041504539710.07331113381150.4892329463830.06886934419110.526077947221-71.500526526119.720024932215.3078846928
100.470006730617-0.1918805635720.01312843974190.31103423373-0.1262085920180.652277195180.0664123203789-0.203057900104-0.002113177610080.279952950922-0.089632958747-0.0405397890506-0.1571608879750.12505881735-2.49778388859E-50.609888034612-0.1663572429170.08070452393340.608476669254-0.03265587763530.54967203855-71.394384282634.739298544427.7957771937
110.9917892461970.00599308970473-0.2337861885790.372360087351-0.6469605464791.081972787980.08206668391480.09041816215960.0221470513093-0.139709916121-0.08940805246820.07318249371720.0991611004088-0.186581860640.0001227398052860.459808673258-0.0914094311592-0.0228964738920.2736646866450.0228106191980.279116727818-91.327405324171.083488201937.4973068061
120.45567436364-0.0848731938772-0.3939461464870.601955243689-0.3397221230510.5887202873580.102445422639-0.2381161488340.007821518175830.170001090086-0.1932821358570.1604569052080.137926968806-0.1692512469218.72351563258E-70.513103669464-0.0490668803409-0.02291119403960.4240927863410.04160017994580.397009523766-83.610055974979.212420161749.2362919247
130.1781382531370.1714521604370.04931624579360.698137761653-0.5043409871220.296916114206-0.0658182156949-0.009405311239130.1184390837680.175962061531-0.02267077636820.1844179187770.132486059661-0.06747895644578.92816412993E-60.476716898038-0.06621462175740.01584132788560.4418943082630.01500886820040.426455109908-89.67100996585.788848334845.2364600464
140.793762476762-0.363045376207-0.7411229187051.006477437820.2123161140730.9966189242890.108154265571-0.0936461275360.174754421168-0.0416381207745-0.118612344359-0.1159478925760.04514831892190.1997795749072.02803737226E-50.472458967746-0.01514151302110.02711983556260.4751024274030.07286679512480.379515837775-76.804367187783.442686398731.9566131668
150.124685810922-0.183741934935-0.120943921920.2585701380640.09744264907471.04064470226-0.0590272245725-0.08956078678750.07002195858180.0663784060195-0.03846218301020.115699353918-0.1342582206090.1454933019745.6444058615E-50.4432177878760.0260426382059-0.09192278168360.432486834755-0.01085892105360.494435057707-65.484169771777.9830865279.1593646023
160.6699334650010.56661763567-0.1924768087020.779620202128-0.3541060839940.326014590583-0.151289427993-0.0307725618060.208914414875-0.0438033327457-0.01853464709690.137856244305-0.03058719218290.1137401417738.42448901526E-50.4457865293950.0922456251523-0.05656253437560.4247355214340.011232385620.477108522992-72.347678195169.82857511866.7631975962
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 159 through 402 )DE159 - 402138 - 381
22chain 'A' and (resid 24 through 84 )AA24 - 841 - 61
33chain 'A' and (resid 85 through 158 )AA85 - 15862 - 135
44chain 'A' and (resid 159 through 294 )AA159 - 294136 - 271
55chain 'A' and (resid 295 through 402 )AA295 - 402272 - 379
66chain 'B' and (resid 23 through 84 )BB23 - 841 - 62
77chain 'B' and (resid 85 through 118 )BB85 - 11863 - 96
88chain 'B' and (resid 119 through 209 )BB119 - 20997 - 187
99chain 'B' and (resid 210 through 294 )BB210 - 294188 - 272
1010chain 'B' and (resid 295 through 402 )BB295 - 402273 - 380
1111chain 'C' and (resid 23 through 84 )CD23 - 841 - 62
1212chain 'C' and (resid 85 through 158 )CD85 - 15863 - 136
1313chain 'C' and (resid 159 through 209 )CD159 - 209137 - 187
1414chain 'C' and (resid 210 through 402 )CD210 - 402188 - 380
1515chain 'D' and (resid 22 through 84 )DE22 - 841 - 63
1616chain 'D' and (resid 85 through 158 )DE85 - 15864 - 137

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