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- PDB-9fhw: Bacteroides ovatus polysaccharide lyase family 38 (BoPL38) wild t... -

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Basic information

Entry
Database: PDB / ID: 9fhw
TitleBacteroides ovatus polysaccharide lyase family 38 (BoPL38) wild type in complex tetraguluronic acid at pH 8
ComponentsAlginate lyase family protein
KeywordsLYASE / polysaccharide lyase / complex / alginate
Function / homologyAlginate lyase domain / Alginate lyase / Chondroitin AC/alginate lyase / periplasmic space / lyase activity / Alginate lyase family protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsTandrup, T. / Wilkens, C.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent ResearchDFF170746 Denmark
Citation
Journal: J.Am.Chem.Soc. / Year: 2025
Title: The Swiss Army Knife of Alginate Metabolism: Mechanistic Analysis of a Mixed-Function Polysaccharide Lyase/Epimerase of the Human Gut Microbiota.
Authors: Tandrup, T. / Rivas-Fernandez, J.P. / Madsen, M. / Ronne, M.E. / B Petersen, A. / Klau, L.J. / Tondervik, A. / Wilkens, C. / Aachmann, F.L. / Rovira, C. / Svensson, B.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMay 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)187,06711
Polymers183,8894
Non-polymers3,1787
Water5,981332
1
A: Alginate lyase family protein
B: Alginate lyase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5826
Polymers91,9442
Non-polymers1,6374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Alginate lyase family protein
D: Alginate lyase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4865
Polymers91,9442
Non-polymers1,5413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)196.935, 89.034, 145.908
Angle α, β, γ (deg.)90.000, 120.362, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and (resid 24 through 402 or resid 500 through 503))
d_3ens_1(chain "C" and (resid 24 through 402 or resid 500 through 503))
d_4ens_1(chain "D" and resid 24 through 503)

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALALYSLYSAA24 - 40224 - 402
d_12LGULGULGULGUEE4
d_13LGULGULGULGUEE3
d_14LGULGULGULGUEE2
d_15LGULGULGULGUEE1
d_21ALAALALYSLYSBB24 - 40224 - 402
d_22LGULGULGULGUFF4
d_23LGULGULGULGUFF3
d_24LGULGULGULGUFF2
d_25LGULGULGULGUFF1
d_31ALAALALYSLYSCC24 - 40224 - 402
d_32LGULGULGULGUGG4
d_33LGULGULGULGUGG3
d_34LGULGULGULGUGG2
d_35LGULGULGULGUGG1
d_41ALAALALYSLYSDD24 - 40224 - 402
d_42LGULGULGULGUHH4
d_43LGULGULGULGUHH3
d_44LGULGULGULGUHH2
d_45LGULGULGULGUHH1

NCS oper:
IDCodeMatrixVector
1given(-0.999976870768, -0.00449474793405, -0.00510442647189), (0.00452764877645, -0.999968933036, -0.00645239180317), (-0.00507526601813, -0.00647535361457, 0.999966155162)-98.5760683804, -127.351388067, -0.573160326914
2given(-0.485969536299, 0.000323984643888, 0.87397568892), (0.00304579895707, 0.999994486507, 0.00132290024069), (-0.873970441662, 0.00330484345836, -0.485967843701)-36.1339830067, 38.6161413176, -105.833320653
3given(0.479860962889, -0.00751362645868, 0.877312374079), (0.00118213616, -0.999956882875, -0.00921058875659), (0.877343751815, 0.00545690467053, -0.479831390534)10.6501860768, -89.0375558055, -19.5547619746

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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) / Strain: CP926 / Gene: F3B53_17925, F3D71_22350 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5M5BWR5
#2: Polysaccharide
alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid- ...alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid


Type: oligosaccharide / Mass: 722.510 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LGulpAa1-4LGulpAa1-4LGulpAa1-4LGulpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a1121A-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-L-GulpA]{[(4+1)][a-L-GulpA]{[(4+1)][a-L-GulpA]{[(4+1)][a-L-GulpA]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3 Å3/Da / Density % sol: 59.01 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: 18% (W/V) PEG3350, 0.2 M (NH4)2SO4 and 0.1 M citric acid pH 3.5 soaked in tetraguluronic acid in 18% (W/V) PEG3350, 0.2 M (NH4)2SO4 and 0.1 M HEPES pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.54→62.95 Å / Num. obs: 71977 / % possible obs: 99.65 % / Redundancy: 7 % / Biso Wilson estimate: 61.02 Å2 / CC1/2: 0.982 / Net I/σ(I): 6.56
Reflection shellResolution: 2.54→2.57 Å / Num. unique obs: 2722 / CC1/2: 0.26

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
xia23.5.0data reduction
xia23.5.0data scaling
PHASER1.21_5207phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→62.95 Å / SU ML: 0.3916 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.6387
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2484 3652 5.09 %
Rwork0.2052 68094 -
obs0.2073 71746 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.65 Å2
Refinement stepCycle: LAST / Resolution: 2.54→62.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12202 0 211 332 12745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008912722
X-RAY DIFFRACTIONf_angle_d1.087217258
X-RAY DIFFRACTIONf_chiral_restr0.05511875
X-RAY DIFFRACTIONf_plane_restr0.00842187
X-RAY DIFFRACTIONf_dihedral_angle_d15.7084702
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.697141900524
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.648492728887
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.713543927093
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.570.31241310.29682503X-RAY DIFFRACTION95.92
2.57-2.610.33471380.29312597X-RAY DIFFRACTION98.99
2.61-2.650.35821370.29472604X-RAY DIFFRACTION99.31
2.65-2.690.34591640.29042574X-RAY DIFFRACTION99.74
2.69-2.730.33291370.2772592X-RAY DIFFRACTION99.89
2.73-2.770.35931490.31622626X-RAY DIFFRACTION99.68
2.77-2.820.37881520.3162563X-RAY DIFFRACTION99.67
2.82-2.870.37391290.30062622X-RAY DIFFRACTION99.75
2.87-2.930.32121680.26752595X-RAY DIFFRACTION99.71
2.93-2.990.29771270.24482651X-RAY DIFFRACTION99.93
2.99-3.050.29421280.24172585X-RAY DIFFRACTION99.85
3.05-3.120.26961300.23362618X-RAY DIFFRACTION99.89
3.12-3.20.32131630.2262615X-RAY DIFFRACTION99.96
3.2-3.290.29881510.23042630X-RAY DIFFRACTION100
3.29-3.380.30111370.24322610X-RAY DIFFRACTION99.93
3.38-3.490.31511330.23112615X-RAY DIFFRACTION100
3.49-3.620.22061330.19322628X-RAY DIFFRACTION99.93
3.62-3.760.22051420.18122626X-RAY DIFFRACTION99.96
3.76-3.930.1931580.16862597X-RAY DIFFRACTION100
3.93-4.140.22041220.16722658X-RAY DIFFRACTION99.93
4.14-4.40.20981120.17352675X-RAY DIFFRACTION100
4.4-4.740.19721330.15342659X-RAY DIFFRACTION99.93
4.74-5.220.19511410.17132645X-RAY DIFFRACTION100
5.22-5.970.23371650.1912619X-RAY DIFFRACTION100
5.97-7.520.25391400.19612666X-RAY DIFFRACTION100
7.52-62.950.19221320.19342721X-RAY DIFFRACTION98.93

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