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

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Basic information

Entry
Database: PDB / ID: 9fhz
TitleBacteroides ovatus polysaccharide lyase family 38 (BoPL38) wild type in complex unsaturated guluronic acid tetramer 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: 1.88 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

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)186,04710
Polymers183,8894
Non-polymers2,1586
Water7,855436
1
A: Alginate lyase family protein
B: Alginate lyase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1115
Polymers91,9442
Non-polymers1,1673
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)92,9355
Polymers91,9442
Non-polymers9913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)198.421, 88.652, 147.307
Angle α, β, γ (deg.)90.000, 120.419, 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 151 or resid 153...
d_2ens_1(chain "B" and (resid 24 through 151 or resid 153...
d_3ens_1(chain "C" and (resid 24 through 151 or resid 153...
d_4ens_1(chain "D" and (resid 24 through 151 or resid 153...

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_11ALAALAALAALAAA24 - 15124 - 151
d_12HISHISARGARGAA153 - 190153 - 190
d_13PHEPHELYSLYSAA192 - 402192 - 402
d_14LGULGULGULGUEE1
d_21ALAALAALAALABB24 - 15124 - 151
d_22HISHISARGARGBB153 - 190153 - 190
d_23PHEPHELYSLYSBB192 - 402192 - 402
d_24LGULGULGULGUFF1
d_31ALAALAALAALACC24 - 15124 - 151
d_32HISHISARGARGCC153 - 190153 - 190
d_33PHEPHELYSLYSCC192 - 402192 - 402
d_34LGULGULGULGUGG1
d_41ALAALAALAALADD24 - 15124 - 151
d_42HISHISARGARGDD153 - 190153 - 190
d_43PHEPHELYSLYSDD192 - 402192 - 402
d_44LGULGULGULGUHH1

NCS oper:
IDCodeMatrixVector
1given(-0.999995651132, 0.00144081493922, 0.00257328002835), (-0.00141649194268, -0.999954541979, 0.00942907876738), (0.00258674860969, 0.00942539273113, 0.999952234211)99.2241682489, -38.4472498243, -0.0905816560946
2given(-0.477699329657, 0.00465702596244, 0.878511048624), (-0.00364364133866, 0.99996684664, -0.00728213561047), (-0.878515836125, -0.00667965047284, -0.477666523787)35.9244113818, 38.6333785942, 107.107960872
3given(0.477862493247, 0.00770646940183, 0.878400846924), (-0.000560936568195, -0.999958635968, 0.00907808912769), (0.87843447274, -0.00483080546105, -0.477838404087)-11.2421393223, -0.0235028716345, 19.9839027126

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Sugars , 3 types, 4 molecules

#2: Polysaccharide 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L- ...4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid


Type: oligosaccharide / Mass: 528.372 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a1121A-1a_1-5][a11eEA-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-L-GulpA]{[(4+1)][a-L-GulpA]{[(4+1)][a-L-4-deoxy-AllpA]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid


Type: oligosaccharide / Mass: 546.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LGulpAa1-4LGulpAa1-4LGulpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1121A-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-L-GulpA]{[(4+1)][a-L-GulpA]{[(4+1)][a-L-GulpA]{}}}LINUCSPDB-CARE
#4: Polysaccharide 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid


Type: oligosaccharide / Mass: 352.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a1121A-1a_1-5][a11eEA-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-GulpA]{[(4+1)][a-L-4-deoxy-AllpA]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 438 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.04 Å3/Da / Density % sol: 59.51 %
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: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.88→52.94 Å / Num. obs: 174260 / % possible obs: 97.1 % / Redundancy: 7.1 % / Biso Wilson estimate: 36.54 Å2 / CC1/2: 0.992 / Net I/σ(I): 8.6
Reflection shellResolution: 1.88→5.1 Å / Num. unique obs: 9217 / CC1/2: 0.281

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
xia23.12data reduction
xia23.12data scaling
PHASER1.21_5207phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→52.94 Å / SU ML: 0.2948 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.1953
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2576 8301 5.01 %
Rwork0.2268 157464 -
obs0.2283 165765 92.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.77 Å2
Refinement stepCycle: LAST / Resolution: 1.88→52.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12202 0 145 436 12783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008112677
X-RAY DIFFRACTIONf_angle_d0.981617187
X-RAY DIFFRACTIONf_chiral_restr0.0531847
X-RAY DIFFRACTIONf_plane_restr0.00882186
X-RAY DIFFRACTIONf_dihedral_angle_d14.31934743
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.752914569853
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.692657136587
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.766256721209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.90.3713720.39991315X-RAY DIFFRACTION23.4
1.9-1.920.4011260.38272411X-RAY DIFFRACTION42.9
1.92-1.950.42691720.36443518X-RAY DIFFRACTION61.54
1.95-1.970.37322350.35344334X-RAY DIFFRACTION77
1.97-20.36843150.34275301X-RAY DIFFRACTION94.8
2-2.020.3752870.31465654X-RAY DIFFRACTION98.69
2.02-2.050.32842900.30455588X-RAY DIFFRACTION99.09
2.05-2.080.33132560.29365572X-RAY DIFFRACTION99.15
2.08-2.120.30843020.27725637X-RAY DIFFRACTION99.26
2.12-2.150.30622680.2635625X-RAY DIFFRACTION99.39
2.15-2.190.31263140.25485592X-RAY DIFFRACTION99.39
2.19-2.230.3052840.24675677X-RAY DIFFRACTION99.4
2.23-2.270.29183090.24785636X-RAY DIFFRACTION99.53
2.27-2.320.26212930.25455639X-RAY DIFFRACTION99.65
2.32-2.370.29112960.24765650X-RAY DIFFRACTION99.73
2.37-2.420.26862660.22995673X-RAY DIFFRACTION99.8
2.42-2.480.27532780.22245667X-RAY DIFFRACTION99.82
2.48-2.550.25332920.22015638X-RAY DIFFRACTION99.78
2.55-2.620.26693080.22565644X-RAY DIFFRACTION99.68
2.62-2.710.27432940.22775693X-RAY DIFFRACTION99.72
2.71-2.810.26133090.22795620X-RAY DIFFRACTION99.61
2.81-2.920.2743040.23555652X-RAY DIFFRACTION99.43
2.92-3.050.27963180.23755625X-RAY DIFFRACTION99.22
3.05-3.210.27022890.22675606X-RAY DIFFRACTION98.93
3.21-3.410.23963040.22265599X-RAY DIFFRACTION97.91
3.41-3.680.25232500.21134965X-RAY DIFFRACTION87.09
3.68-4.050.21853320.19975662X-RAY DIFFRACTION99.52
4.05-4.630.23123510.19265631X-RAY DIFFRACTION99.95
4.63-5.830.22292840.20145780X-RAY DIFFRACTION99.98
5.84-52.940.22553030.21725860X-RAY DIFFRACTION99.79

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