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- PDB-6t8i: Crystal structure of wild type EndoBT-3987 from Bacteroides theta... -

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Basic information

Entry
Database: PDB / ID: 6t8i
TitleCrystal structure of wild type EndoBT-3987 from Bacteroides thetaiotamicron VPI-5482
ComponentsEndo-beta-N-acetylglucosaminidase F1
KeywordsHYDROLASE / endo-b-N-acetylglucosaminidase / EndoBT / glycoside hydrolase
Function / homology
Function and homology information


hypothetical protein (bacova_03559) / Domain of unknown function DUF1735 / BT_3987-like, N-terminal domain / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich ...hypothetical protein (bacova_03559) / Domain of unknown function DUF1735 / BT_3987-like, N-terminal domain / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Endo-beta-N-acetylglucosaminidase F1
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTrastoy, B. / Du, J.J. / Klontz, E.H. / Cifuente, J.O. / Sundberg, E.J. / Guerin, M.E.
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis of mammalian high-mannose N-glycan processing by human gut Bacteroides.
Authors: Trastoy, B. / Du, J.J. / Klontz, E.H. / Li, C. / Cifuente, J.O. / Wang, L.X. / Sundberg, E.J. / Guerin, M.E.
History
DepositionOct 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endo-beta-N-acetylglucosaminidase F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3783
Polymers49,1941
Non-polymers1842
Water4,882271
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-1 kcal/mol
Surface area17830 Å2
Unit cell
Length a, b, c (Å)74.578, 74.578, 133.540
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 Endo-beta-N-acetylglucosaminidase F1


Mass: 49193.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_3987 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A0N4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 200 mM sodium bromide, and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.4→58.143 Å / Num. obs: 85242 / % possible obs: 100 % / Redundancy: 9.8 % / CC1/2: 1 / Rmerge(I) obs: 0.044 / Net I/σ(I): 24.5
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 8417 / CC1/2: 0.942

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIX1.14_3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3POH

3poh


Resolution: 1.4→58.143 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1812 4246 4.98 %
Rwork0.163 80984 -
obs0.1639 85230 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.79 Å2 / Biso mean: 25.6811 Å2 / Biso min: 10.77 Å2
Refinement stepCycle: final / Resolution: 1.4→58.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 27 271 3592
Biso mean--26.47 31.18 -
Num. residues----434
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.4-1.41590.21491350.22666
1.4159-1.43260.23071510.19272653
1.4326-1.45010.20831070.19142702
1.4501-1.46840.22251330.18092663
1.4684-1.48780.20861030.182712
1.4878-1.50810.23171250.17722680
1.5081-1.52970.18051260.16682682
1.5297-1.55250.16781550.16592680
1.5525-1.57680.18761480.16712667
1.5768-1.60260.19911230.16542651
1.6026-1.63030.20781530.1672697
1.6303-1.65990.17181690.16672647
1.6599-1.69180.16951490.16532645
1.6918-1.72640.17211330.16012685
1.7264-1.76390.19361770.16532642
1.7639-1.8050.17361330.15972708
1.805-1.85010.17831430.15772666
1.8501-1.90010.18241210.15612737
1.9001-1.9560.16331470.15322677
1.956-2.01920.19071770.15222685
2.0192-2.09130.14931330.14932666
2.0913-2.17510.1671530.15342670
2.1751-2.27410.16471190.15622762
2.2741-2.3940.17881510.15412693
2.394-2.5440.19431650.16072698
2.544-2.74040.19621370.16562742
2.7404-3.01620.17931270.16322745
3.0162-3.45260.18621430.15782764
3.4526-4.34960.15581600.14962778
4.3496-4.34960.20531500.18742921
Refinement TLS params.Method: refined / Origin x: 57.1832 Å / Origin y: 19.8188 Å / Origin z: 63.9391 Å
111213212223313233
T0.1778 Å2-0.0474 Å20.0131 Å2-0.0874 Å2-0.0138 Å2--0.1543 Å2
L0.6261 °20.1438 °2-0.2534 °2-0.4309 °2-0.1848 °2--1.03 °2
S-0.0271 Å °0.0301 Å °-0.0027 Å °-0.1121 Å °0.002 Å °-0.0223 Å °0.0911 Å °0.0341 Å °0.0241 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA43 - 476
2X-RAY DIFFRACTION1allA701
3X-RAY DIFFRACTION1allS3 - 501

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