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- PDB-6mly: Bifunctional GH43-CE Bacteroides eggerthii, BACEGG_01304 -

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Basic information

Entry
Database: PDB / ID: 6mly
TitleBifunctional GH43-CE Bacteroides eggerthii, BACEGG_01304
ComponentsBifunctional GH43-CE protein
KeywordsHYDROLASE / glycoside hydrolase / GH43 / carbohydrate esterase
Function / homology
Function and homology information


xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
: / Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / : / BD-FAE / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / alpha/beta hydrolase fold / Glycosyl hydrolase domain; family 43 / 5 Propeller ...: / Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / : / BD-FAE / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / alpha/beta hydrolase fold / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Concanavalin A-like lectin/glucanase domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Glycoside hydrolase / Glycoside hydrolase
Similarity search - Component
Biological speciesBacteroides eggerthii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKoropatkin, N.M. / Pereira, G.V. / Cann, I.
CitationJournal: Nat Commun / Year: 2021
Title: Degradation of complex arabinoxylans by human colonic Bacteroidetes
Authors: Pereira, G.V. / DAlessandro-Gabazza, C. / Farris, J. / Wefers, D. / Mackie, R. / Koropatkin, N.M. / Gabazza, E.C. / Cann, I.
History
DepositionSep 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional GH43-CE protein
B: Bifunctional GH43-CE protein
C: Bifunctional GH43-CE protein
D: Bifunctional GH43-CE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,05421
Polymers359,1674
Non-polymers88717
Water7,134396
1
A: Bifunctional GH43-CE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9985
Polymers89,7921
Non-polymers2064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional GH43-CE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9364
Polymers89,7921
Non-polymers1443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bifunctional GH43-CE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9985
Polymers89,7921
Non-polymers2064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bifunctional GH43-CE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1227
Polymers89,7921
Non-polymers3306
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)254.734, 93.310, 214.039
Angle α, β, γ (deg.)90.000, 123.380, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Bifunctional GH43-CE protein


Mass: 89791.820 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides eggerthii (bacteria) / Gene: xynB_2, NCTC11155_00458 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A380YKU1, UniProt: E5WZQ7*PLUS, xylan 1,4-beta-xylosidase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O
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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 6.5
Details: 0.2M AmSO4, 0.1M MES pH 6.5, 30% PEG 5k; streak seeding to produce larger crystals
Temp details: room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 7, 2018
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 113694 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.103 / Rrim(I) all: 0.192 / Χ2: 2.071 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.753.11.10556710.4660.7461.3380.84199.9
2.75-2.83.21.02756420.5330.6821.2360.877100
2.8-2.853.20.87556260.610.5791.0530.872100
2.85-2.913.30.7356580.6690.4810.8770.884100
2.91-2.973.30.63856710.7250.4180.7650.898100
2.97-3.043.30.54356900.7810.3540.650.94100
3.04-3.123.30.45556410.8520.2950.5440.944100
3.12-3.23.40.39657010.8550.2570.4740.964100
3.2-3.33.40.31856520.9010.2060.380.974100
3.3-3.43.40.25156230.9390.1610.2991.004100
3.4-3.523.40.20157100.8470.1290.241.072100
3.52-3.663.40.16756760.9280.1060.1991.103100
3.66-3.833.40.14156930.980.0890.1671.19999.9
3.83-4.033.50.12156870.9830.0760.1441.28699.9
4.03-4.293.50.09956990.9860.0620.1171.49199.9
4.29-4.623.50.07757040.9920.0480.0911.58299.7
4.62-5.083.50.06456730.9940.040.0761.66499.7
5.08-5.813.50.06457340.9940.040.0751.72599.5
5.81-7.323.50.05857130.9920.0360.0682.33299.3
7.32-503.40.05558300.9840.0350.06518.09598.6

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZXL

3zxl


Resolution: 2.7→48.16 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.892 / SU B: 44.282 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.351
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2686 5719 5 %RANDOM
Rwork0.2198 ---
obs0.2222 107971 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 257.19 Å2 / Biso mean: 62.463 Å2 / Biso min: 36.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å23.78 Å2
2---7.08 Å20 Å2
3---1.68 Å2
Refinement stepCycle: final / Resolution: 2.7→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23692 0 56 396 24144
Biso mean--57.88 62.19 -
Num. residues----3029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01424349
X-RAY DIFFRACTIONr_bond_other_d0.0010.01721577
X-RAY DIFFRACTIONr_angle_refined_deg0.961.65432966
X-RAY DIFFRACTIONr_angle_other_deg0.7141.64350417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6353017
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0522.6341230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.835153896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.21715120
X-RAY DIFFRACTIONr_chiral_restr0.0440.23064
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0227499
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024865
X-RAY DIFFRACTIONr_rigid_bond_restr2.298345926
X-RAY DIFFRACTIONr_sphericity_free73.4855303
X-RAY DIFFRACTIONr_sphericity_bonded23.149545418
LS refinement shellResolution: 2.703→2.773 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 406 -
Rwork0.318 6923 -
all-7329 -
obs--86.48 %
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)
11.09780.46971.19010.31680.60341.37330.17130.0435-0.01650.2258-0.15710.0080.3448-0.16-0.01410.8513-0.2969-0.14651.0939-0.00220.0452-36.305921.886240.9369
20.67460.07880.93610.27490.0761.4432-0.0010.14550.01050.03030.02780.0741-0.07230.0188-0.02680.4371-0.0022-0.10080.51190.03720.0725-19.8728-22.680445.2291
30.46540.249-0.85380.213-0.58211.90160.03060.11820.01970.07290.0411-0.0294-0.09770.0021-0.07160.58090.0165-0.13890.5836-0.02560.123524.798944.694145.5872
40.93720.3596-1.26950.1997-0.63442.1052-0.05260.16410.02960.07240.0301-0.0302-0.0661-0.05790.02250.49950.0101-0.12490.5746-0.01580.098841.537-1.187648.475
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 788
2X-RAY DIFFRACTION2B25 - 788
3X-RAY DIFFRACTION3C23 - 788
4X-RAY DIFFRACTION4D25 - 788

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