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- PDB-9h6f: Bacteroides ovatus GH98 endoxylanase in complex with arabino-xylo... -

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Basic information

Entry
Database: PDB / ID: 9h6f
TitleBacteroides ovatus GH98 endoxylanase in complex with arabino-xylooligosaccharide
ComponentsGlycosyl hydrolase family 98
KeywordsHYDROLASE / Endoxylanase / Carbohydrate hydrolase / GH98
Function / homology
Function and homology information


carbohydrate binding / carbohydrate metabolic process / hydrolase activity
Similarity search - Function
Domain of unknown function DUF4988 / Domain of unknown function / Glycosyl hydrolase family 98, C-terminal / Glycosyl hydrolase family 98, central domain / Glycosyl hydrolase family 98 / Glycosyl hydrolase family 98 C-terminal domain / Polysaccharide lyase family 8-like, C-terminal / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
alpha-L-arabinofuranose / beta-D-xylopyranose / Glycoside hydrolase family 98 domain-containing protein
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTomlinson, C.W.E. / Cartmell, A. / Bolam, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Bacteroides ovatus GH98 endoxylanase in complex with arabino-xylooligosaccharide
Authors: Tomlinson, C.W.E. / Cartmell, A. / Bolam, D.
History
DepositionOct 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 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: Glycosyl hydrolase family 98
B: Glycosyl hydrolase family 98
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,9278
Polymers201,8502
Non-polymers1,0776
Water9,620534
1
A: Glycosyl hydrolase family 98
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6624
Polymers100,9251
Non-polymers7373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyl hydrolase family 98
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,2664
Polymers100,9251
Non-polymers3403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.05, 63.85, 180.49
Angle α, β, γ (deg.)90, 118.69, 90
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 45 - 939 / Label seq-ID: 1 - 895

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycosyl hydrolase family 98


Mass: 100925.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: F3F51_01075, HUV13_02585 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6N3VET1

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Sugars , 3 types, 4 molecules

#2: Polysaccharide beta-D-xylopyranose-(1-3)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 546.474 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DXylpb1-3DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a212h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(3+1)][b-D-Xylp]{}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-AHR / alpha-L-arabinofuranose / alpha-L-arabinose / L-arabinose / arabinose


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LArafaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-arabinofuranoseCOMMON NAMEGMML 1.0
a-L-ArafIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 536 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: Vapour diffusion

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.93932 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93932 Å / Relative weight: 1
ReflectionResolution: 2.2→59.18 Å / Num. obs: 94781 / % possible obs: 99.9 % / Redundancy: 1.9 % / CC1/2: 0.995 / Χ2: 1.28 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Χ2% possible all
12.05-59.181.8286320.9990.6498.3
2.2-2.2421.446210.6431.03100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
REFMAC5.8.0430 (refmacat 0.4.88)refinement
XDSdata reduction
Cootmodel building
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→59.176 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.187 / SU B: 15.063 / SU ML: 0.191 / Average fsc free: 0.9537 / Average fsc work: 0.9702 / Cross valid method: FREE R-VALUE / ESU R: 0.301 / ESU R Free: 0.223
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2454 4758 5.02 %
Rwork0.1922 90021 -
all0.195 --
obs-94779 99.924 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 40.87 Å2
Baniso -1Baniso -2Baniso -3
1-1.257 Å20 Å2-1.005 Å2
2--0.671 Å20 Å2
3----0.518 Å2
Refinement stepCycle: LAST / Resolution: 2.2→59.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14243 0 69 534 14846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01214723
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613328
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.79820045
X-RAY DIFFRACTIONr_angle_other_deg0.561.75830718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.00751794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.501567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.351102346
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.57410720
X-RAY DIFFRACTIONr_chiral_restr0.0770.22183
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217552
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023548
X-RAY DIFFRACTIONr_nbd_refined0.2090.22737
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.212077
X-RAY DIFFRACTIONr_nbtor_refined0.1850.27192
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.27602
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2633
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0470.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1340.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2480.220
X-RAY DIFFRACTIONr_nbd_other0.190.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1750.219
X-RAY DIFFRACTIONr_mcbond_it2.0152.1377173
X-RAY DIFFRACTIONr_mcbond_other2.0142.1377173
X-RAY DIFFRACTIONr_mcangle_it3.3013.8328968
X-RAY DIFFRACTIONr_mcangle_other3.33.8328969
X-RAY DIFFRACTIONr_scbond_it2.1272.297550
X-RAY DIFFRACTIONr_scbond_other2.1272.297551
X-RAY DIFFRACTIONr_scangle_it3.3974.1311077
X-RAY DIFFRACTIONr_scangle_other3.3974.1311078
X-RAY DIFFRACTIONr_lrange_it5.33420.81716343
X-RAY DIFFRACTIONr_lrange_other5.31920.58216249
X-RAY DIFFRACTIONr_ncsr_local_group_10.0760.0530304
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.075640.05011
12BX-RAY DIFFRACTIONLocal ncs0.075640.05011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.2-2.2570.3193530.29565690.29669230.9250.93599.98560.288
2.257-2.3190.2943320.25864160.2667490.9370.95399.98520.25
2.319-2.3860.2823350.23763040.2466390.9480.9621000.228
2.386-2.4590.2823400.2361160.23264560.9450.9651000.217
2.459-2.540.2823500.21858060.22261580.9460.96999.96750.203
2.54-2.6290.2663170.21456810.21760000.9570.97299.96670.201
2.629-2.7280.282920.2155690.21358630.9540.97399.96590.194
2.728-2.8390.2662820.252860.20355710.9550.97699.94610.185
2.839-2.9650.2672230.20351530.20653760.9530.9741000.187
2.965-3.1090.262460.19449040.19751500.9590.9771000.182
3.109-3.2770.2872060.21146950.21549020.9420.97299.97960.202
3.277-3.4750.2392340.19643860.19846200.9660.9791000.191
3.475-3.7140.2172040.18441630.18543680.9730.98199.97710.178
3.714-4.010.2332060.17338630.17640730.9660.9899.90180.171
4.01-4.3910.2012030.15935480.16137580.9730.98499.81370.164
4.391-4.9060.1821870.13932360.14134450.9790.98899.36140.147
4.906-5.6580.211320.15828610.1630040.9710.98699.63380.167
5.658-6.9140.2481370.17524320.17925710.9690.98199.92220.183
6.914-9.7120.2311140.16719110.1720260.9670.98199.95060.182
9.712-59.1760.268650.22111220.22411920.9480.96599.58050.244
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)
10.8616-0.228-0.03530.6469-0.0120.4386-0.0064-0.0398-0.0282-0.1342-0.0189-0.0364-0.01560.04380.02540.1127-0.033-0.03530.15280.01460.03137.456112.664459.5823
20.72440.23330.02831.1294-0.07870.60340.00480.1134-0.00620.26050.02050.04540.0273-0.0441-0.02520.15640.0306-0.00250.2153-0.00020.004840.1281-17.655319.0958
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA45 - 939
2X-RAY DIFFRACTION2ALLB45 - 939

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