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

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Basic information

Entry
Database: PDB / ID: 6mot
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: 1.71 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3455
Polymers41,0971
Non-polymers2484
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Isoamylase N-terminal domain protein
hetero molecules

A: Isoamylase N-terminal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,69010
Polymers82,1942
Non-polymers4978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_556-x+y,y,-z+11
Buried area3470 Å2
ΔGint-21 kcal/mol
Surface area27560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.959, 99.959, 164.204
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-508-

HOH

21A-728-

HOH

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Components

#1: Protein Isoamylase N-terminal domain protein / Feruloyl esterase


Mass: 41096.961 Da / Num. of mol.: 1
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 / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 306 / 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: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.5M Lithium sulfate, 0.1 M sodium acetate (Hampton SaltRx B10)
Temp details: room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: RAYONIX MX300HE / 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: 1.71→86.567 Å / Num. obs: 99242 / % possible obs: 99.98 % / Redundancy: 40.4 % / Biso Wilson estimate: 24.58 Å2 / Net I/σ(I): 19.3
Reflection shellResolution: 1.71→1.73 Å

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
xia2data scaling
SOLVEphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.71→86.567 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 19.52
RfactorNum. reflection% reflection
Rfree0.1912 3730 3.76 %
Rwork0.1706 --
obs0.1713 99242 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.59 Å2 / Biso mean: 32.1501 Å2 / Biso min: 15.13 Å2
Refinement stepCycle: final / Resolution: 1.71→86.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 0 40 306 3100
Biso mean--46.22 44.34 -
Num. residues----345
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
1.71-1.73170.31221430.352335563699
1.7317-1.75440.33351380.340235313669
1.7544-1.77850.37211400.329635573697
1.7785-1.80390.33661360.309334883624
1.8039-1.83080.34611430.292835553698
1.8308-1.85940.26111350.266335133648
1.8594-1.88990.27071380.246635743712
1.8899-1.92250.22511380.222935453683
1.9225-1.95750.24181380.214235343672
1.9575-1.99510.22851350.200535103645
1.9951-2.03580.20181400.183435703710
2.0358-2.08010.24011340.184735023636
2.0801-2.12850.22081380.178235603698
2.1285-2.18170.20651380.162635063644
2.1817-2.24070.21521390.154235343673
2.2407-2.30670.18331360.156535523688
2.3067-2.38110.17541400.165135303670
2.3811-2.46620.19761390.160735233662
2.4662-2.5650.17071350.162135733708
2.565-2.68170.20951380.167335133651
2.6817-2.82310.21531390.173135273666
2.8231-30.18061410.163335443685
3-3.23170.18481310.159235563687
3.2317-3.55690.15551350.151535383673
3.5569-4.07160.13871410.138235223663
4.0716-5.12970.14381360.122335493685
5.1297-86.67810.18391460.169235503696
Refinement TLS params.Method: refined / Origin x: 9.934 Å / Origin y: 33.1527 Å / Origin z: 69.9878 Å
111213212223313233
T0.1648 Å2-0.0367 Å20.0092 Å2-0.1832 Å2-0.015 Å2--0.1425 Å2
L1.3409 °2-0.5862 °2-0.5434 °2-1.0518 °20.3473 °2--1.0092 °2
S-0.0557 Å °0.067 Å °-0.0456 Å °-0.0461 Å °0.0698 Å °-0.0498 Å °0.0189 Å °0.0025 Å °-0.0162 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA25 - 384
2X-RAY DIFFRACTION1allS1 - 386
3X-RAY DIFFRACTION1allS389 - 391
4X-RAY DIFFRACTION1allS392
5X-RAY DIFFRACTION1allB1 - 3
6X-RAY DIFFRACTION1allB4

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