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

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Basic information

Entry
Database: PDB / ID: 9fhu
TitleBacteroides ovatus polysaccharide lyase family 38 (BoPL38) wild type in complex hexamannuluronic acid at pH 3.5
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: 2.09 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)187,45115
Polymers183,8894
Non-polymers3,56211
Water18,9701053
1
A: Alginate lyase family protein
B: Alginate lyase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7748
Polymers91,9442
Non-polymers1,8296
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)93,6787
Polymers91,9442
Non-polymers1,7335
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)197.843, 89.013, 146.819
Angle α, β, γ (deg.)90.000, 120.491, 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_1(chain "A" and (resid 24 through 44 or resid 46...
d_2ens_1(chain "B" and (resid 24 through 44 or resid 46...
d_3ens_1(chain "C" and (resid 24 through 44 or resid 46...
d_4ens_1(chain "D" and (resid 24 through 44 or resid 46...

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_11ALAALAGLYGLYAA24 - 4424 - 44
d_12LYSLYSSERSERAA46 - 6946 - 69
d_13THRTHRALAALAAA71 - 15171 - 151
d_14HISHISALAALAAA153 - 199153 - 199
d_15LEULEUGLYGLYAA201 - 204201 - 204
d_16LYSLYSILEILEAA206 - 264206 - 264
d_17GLUGLUALAALAAA266 - 268266 - 268
d_18GLNGLNGLNGLNAA270270
d_19ILEILEPROPROAA272 - 274272 - 274
d_110METMETSERSERAA276 - 314276 - 314
d_111ILEILEALAALAAA316 - 362316 - 362
d_112LEULEUVALVALAA364 - 393364 - 393
d_113THRTHRLYSLYSAA395 - 403395 - 403
d_114BEMBEMBEMBEMEE1
d_115BEMBEMBEMBEMEE2
d_116BEMBEMBEMBEMEE3
d_117BEMBEMBEMBEMEE4
d_21ALAALAGLYGLYBB24 - 4424 - 44
d_22LYSLYSSERSERBB46 - 6946 - 69
d_23THRTHRALAALABB71 - 15171 - 151
d_24HISHISALAALABB153 - 199153 - 199
d_25LEULEUGLYGLYBB201 - 204201 - 204
d_26LYSLYSILEILEBB206 - 264206 - 264
d_27GLUGLUALAALABB266 - 268266 - 268
d_28GLNGLNGLNGLNBB270270
d_29ILEILEPROPROBB272 - 274272 - 274
d_210METMETSERSERBB276 - 314276 - 314
d_211ILEILEALAALABB316 - 362316 - 362
d_212LEULEUVALVALBB364 - 393364 - 393
d_213THRTHRLYSLYSBB395 - 403395 - 403
d_214BEMBEMBEMBEMFF1
d_215BEMBEMBEMBEMFF2
d_216BEMBEMBEMBEMFF3
d_217BEMBEMBEMBEMFF4
d_31ALAALAGLYGLYCC24 - 4424 - 44
d_32LYSLYSSERSERCC46 - 6946 - 69
d_33THRTHRALAALACC71 - 15171 - 151
d_34HISHISALAALACC153 - 199153 - 199
d_35LEULEUGLYGLYCC201 - 204201 - 204
d_36LYSLYSILEILECC206 - 264206 - 264
d_37GLUGLUALAALACC266 - 268266 - 268
d_38GLNGLNGLNGLNCC270270
d_39ILEILEPROPROCC272 - 274272 - 274
d_310METMETSERSERCC276 - 314276 - 314
d_311ILEILEALAALACC316 - 362316 - 362
d_312LEULEUVALVALCC364 - 393364 - 393
d_313THRTHRLYSLYSCC395 - 403395 - 403
d_314BEMBEMBEMBEMGG1
d_315BEMBEMBEMBEMGG2
d_316BEMBEMBEMBEMGG3
d_317BEMBEMBEMBEMGG4
d_41ALAALAGLYGLYDD24 - 4424 - 44
d_42LYSLYSSERSERDD46 - 6946 - 69
d_43THRTHRALAALADD71 - 15171 - 151
d_44HISHISALAALADD153 - 199153 - 199
d_45LEULEUGLYGLYDD201 - 204201 - 204
d_46LYSLYSILEILEDD206 - 264206 - 264
d_47GLUGLUALAALADD266 - 268266 - 268
d_48GLNGLNGLNGLNDD270270
d_49ILEILEPROPRODD272 - 274272 - 274
d_410METMETSERSERDD276 - 314276 - 314
d_411ILEILEALAALADD316 - 362316 - 362
d_412LEULEUVALVALDD364 - 393364 - 393
d_413THRTHRLYSLYSDD395 - 403395 - 403
d_414BEMBEMBEMBEMHH1
d_415BEMBEMBEMBEMHH2
d_416BEMBEMBEMBEMHH3
d_417BEMBEMBEMBEMHH4

NCS oper:
IDCodeMatrixVector
1given(-0.99998097592, 0.00368803197343, -0.00494431177772), (-0.00372898452222, -0.999958607393, 0.00829928762567), (-0.00491349908165, 0.00831756700145, 0.999953336714)-99.1585495645, 73.6651219859, -0.665998010048
2given(-0.483835123538, 0.00384493251224, 0.875150724004), (0.000923809818684, 0.999992035654, -0.00388268004461), (-0.875158682644, -0.00107010414738, -0.483834822094)-110.778470788, 38.5646017742, 20.0465693314
3given(0.473316689212, 0.00370557009418, 0.880884544344), (-0.00484605370529, -0.999965066632, 0.00681038029353), (0.880879008421, -0.00749228046286, -0.473282197274)-63.3330530652, 112.187830581, 107.081951608

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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
beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid- ...beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 722.510 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a1122A-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1053 / 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: 3.03 Å3/Da / Density % sol: 59.39 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 18% (W/V) PEG3350, 0.2 M (NH4)2SO4 and 0.1 M citric acid pH 3.5

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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: May 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.09→48.93 Å / Num. obs: 250878 / % possible obs: 99.37 % / Redundancy: 1 % / Biso Wilson estimate: 36.28 Å2 / CC1/2: 1 / Net I/σ(I): 9.56
Reflection shellResolution: 2.09→2.12 Å / Num. unique obs: 6533 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSjan 10, 2022data reduction
XSCALEjan 10, 2022data scaling
PHASER1.21_5207phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→48.93 Å / SU ML: 0.2741 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.6018
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2483 6377 4.95 %
Rwork0.2058 122349 -
obs0.208 128726 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.18 Å2
Refinement stepCycle: LAST / Resolution: 2.09→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12238 0 231 1053 13522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007712884
X-RAY DIFFRACTIONf_angle_d0.983817498
X-RAY DIFFRACTIONf_chiral_restr0.05351898
X-RAY DIFFRACTIONf_plane_restr0.00852217
X-RAY DIFFRACTIONf_dihedral_angle_d17.96425150
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.664318222327
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.721718623553
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.59374803749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.120.31831780.25283400X-RAY DIFFRACTION83.44
2.12-2.140.30632270.24624024X-RAY DIFFRACTION100
2.14-2.170.30712340.24844122X-RAY DIFFRACTION99.91
2.17-2.190.29932060.23684058X-RAY DIFFRACTION100
2.19-2.220.28822150.24044090X-RAY DIFFRACTION99.98
2.22-2.250.29912160.23414087X-RAY DIFFRACTION99.98
2.25-2.290.28182050.22824084X-RAY DIFFRACTION99.98
2.29-2.320.28211940.2314124X-RAY DIFFRACTION100
2.32-2.360.3022200.22674091X-RAY DIFFRACTION100
2.36-2.40.28192150.2234031X-RAY DIFFRACTION100
2.4-2.440.28442130.21434113X-RAY DIFFRACTION99.98
2.44-2.480.2742170.2154113X-RAY DIFFRACTION99.95
2.48-2.530.29082110.22054071X-RAY DIFFRACTION99.95
2.53-2.580.28681660.22174127X-RAY DIFFRACTION99.98
2.58-2.640.25522400.2134067X-RAY DIFFRACTION99.98
2.64-2.70.25892130.21514101X-RAY DIFFRACTION99.95
2.7-2.770.26312070.20994093X-RAY DIFFRACTION99.98
2.77-2.840.24612150.22054075X-RAY DIFFRACTION99.95
2.84-2.920.29922070.22854109X-RAY DIFFRACTION100
2.92-3.020.29372000.23394122X-RAY DIFFRACTION99.93
3.02-3.130.26262140.22864090X-RAY DIFFRACTION99.98
3.13-3.250.24472090.21824108X-RAY DIFFRACTION99.86
3.25-3.40.25892250.21294095X-RAY DIFFRACTION99.88
3.4-3.580.25362080.1994118X-RAY DIFFRACTION99.91
3.58-3.80.21511800.18594126X-RAY DIFFRACTION99.79
3.8-4.10.21072020.1784118X-RAY DIFFRACTION99.65
4.1-4.510.2042320.17284126X-RAY DIFFRACTION99.68
4.51-5.160.21952320.17254116X-RAY DIFFRACTION99.93
5.16-6.50.21532410.20064115X-RAY DIFFRACTION99.86
6.5-48.930.23862350.20584235X-RAY DIFFRACTION99.67

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