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- PDB-6mou: Bacteroides intestinalis feruloyl esterase, Bacint_01033 -

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Basic information

Entry
Database: PDB / ID: 6mou
TitleBacteroides intestinalis feruloyl esterase, Bacint_01033
ComponentsIsoamylase N-terminal domain protein
KeywordsHYDROLASE / carbohydrate esterase / feruloyl esterase
Function / homologyEsterase-like / Putative esterase / Immunoglobulin E-set / Alpha/Beta hydrolase fold / Immunoglobulin-like fold / Isoamylase N-terminal domain protein
Function and homology information
Biological speciesBacteroides intestinalis DSM 17393 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.24 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
DepositionOct 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoamylase N-terminal domain protein
B: Isoamylase N-terminal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4356
Polymers87,1862
Non-polymers2484
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-13 kcal/mol
Surface area29260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.206, 95.206, 202.609
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Isoamylase N-terminal domain protein


Mass: 43593.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides intestinalis DSM 17393 (bacteria)
Gene: BACINT_01033 / Production host: Escherichia coli (E. coli) / References: UniProt: B3C969
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O

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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: 3.24 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 20% PEG 1,500. Hampton PegRx screen well B8
Temp details: room

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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-F / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / 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: 2.24→76.37 Å / Num. obs: 98838 / % possible obs: 100 % / Redundancy: 5.8 % / Biso Wilson estimate: 30.87 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.18 / Net I/σ(I): 7.5
Reflection shellResolution: 2.24→2.32 Å / Rmerge(I) obs: 0.78 / CC1/2: 0.573

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Processing

Software
NameVersionClassification
d*TREKdata reduction
xia2data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.24→76.369 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.27
RfactorNum. reflection% reflection
Rfree0.236 3788 3.83 %
Rwork0.1903 --
obs0.192 98829 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.13 Å2 / Biso mean: 32.7476 Å2 / Biso min: 17.55 Å2
Refinement stepCycle: final / Resolution: 2.24→76.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5702 0 40 445 6187
Biso mean--44.53 36.02 -
Num. residues----713
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.24-2.26840.42181340.31735633697
2.2684-2.29820.36121400.307634733613
2.2982-2.32970.32071480.294335873735
2.3297-2.3630.29851400.279734383578
2.363-2.39830.31871500.270935723722
2.3983-2.43570.26881380.266935263664
2.4357-2.47570.32191300.273134303560
2.4757-2.51840.35561460.253335673713
2.5184-2.56420.29181460.25635543700
2.5642-2.61350.33061360.239934803616
2.6135-2.66680.3331360.239235383674
2.6668-2.72480.29141400.238335493689
2.7248-2.78820.2691400.226835013641
2.7882-2.85790.28821440.226935023646
2.8579-2.93520.25521400.21335383678
2.9352-3.02160.25021420.206735303672
3.0216-3.11910.27651360.197535163652
3.1191-3.23060.24571480.195635023650
3.2306-3.35990.21211340.182935273661
3.3599-3.51290.23661480.180335283676
3.5129-3.69810.21271380.162334983636
3.6981-3.92970.18981330.14835343667
3.9297-4.23310.16721420.137335033645
4.2331-4.65910.13941390.118135203659
4.6591-5.33310.18231460.128835323678
5.3331-6.71850.18091320.158335313663
6.7185-76.41380.20181420.169735023644

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