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- PDB-6ne9: Bacteroides intestinalis acetyl xylan esterase (BACINT_01039) -

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Basic information

Entry
Database: PDB / ID: 6ne9
TitleBacteroides intestinalis acetyl xylan esterase (BACINT_01039)
ComponentsIsoamylase protein
KeywordsHYDROLASE / carbohydrate esterase family 1
Function / homology: / Esterase-like / Putative esterase / acyltransferase activity, transferring groups other than amino-acyl groups / Immunoglobulin E-set / Alpha/Beta hydrolase fold / Immunoglobulin-like fold / DI(HYDROXYETHYL)ETHER / Putative esterase
Function and homology information
Biological speciesBacteroides intestinalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.738 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
DepositionDec 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 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 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoamylase protein
B: Isoamylase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,63124
Polymers86,9062
Non-polymers1,72522
Water8,773487
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-18 kcal/mol
Surface area28350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.703, 126.553, 110.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-722-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Isoamylase protein


Mass: 43453.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides intestinalis (bacteria) / Gene: HMPREF2531_02003 / Production host: Escherichia coli (E. coli) / References: UniProt: B3C975*PLUS

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Non-polymers , 5 types, 509 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 mM Ammonium sulfate, 80 mM Sodium Cacodylate pH 6.5, and 21% PEG4000
Temp details: room temp

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.738→28.6 Å / Num. obs: 145030 / % possible obs: 91.71 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 15.3
Reflection shellResolution: 1.738→1.8 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.2286 / Num. unique obs: 2851 / % possible all: 28.61

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
SCALEPACKdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.738→28.598 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.96
RfactorNum. reflection% reflection
Rfree0.2169 3859 5.01 %
Rwork0.1829 --
obs0.1846 76952 91.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.93 Å2 / Biso mean: 26.2957 Å2 / Biso min: 7.58 Å2
Refinement stepCycle: final / Resolution: 1.738→28.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5562 0 262 487 6311
Biso mean--38.36 33 -
Num. residues----705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045815
X-RAY DIFFRACTIONf_angle_d0.9277837
X-RAY DIFFRACTIONf_chiral_restr0.035799
X-RAY DIFFRACTIONf_plane_restr0.0041019
X-RAY DIFFRACTIONf_dihedral_angle_d13.1472113
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7381-1.75930.558260.261728829410
1.7593-1.78160.3471340.287681785129
1.7816-1.8050.3357690.27791601167056
1.805-1.82970.27851110.26812420253186
1.8297-1.85590.2821580.25072657281595
1.8559-1.88360.27661560.24692757291398
1.8836-1.9130.26991430.22922833297699
1.913-1.94430.28261230.222528102933100
1.9443-1.97790.26221480.216828032951100
1.9779-2.01380.24131600.204627892949100
2.0138-2.05250.24111420.205228552997100
2.0525-2.09440.20681290.193828342963100
2.0944-2.13990.24421290.194628322961100
2.1399-2.18970.22161580.194328463004100
2.1897-2.24440.2441530.193428132966100
2.2444-2.30510.23721430.184728262969100
2.3051-2.37290.20851660.183628142980100
2.3729-2.44950.24131680.18652813298199
2.4495-2.5370.22371570.182528202977100
2.537-2.63850.21871650.17228272992100
2.6385-2.75840.19931610.169528262987100
2.7584-2.90370.19321510.167128472998100
2.9037-3.08550.21911550.1728633018100
3.0855-3.32340.19841440.168528763020100
3.3234-3.65720.19431220.157528943016100
3.6572-4.1850.18461590.155428703029100
4.185-5.26730.19761620.15182867302998
5.2673-28.60140.19871870.203529953182100

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