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- PDB-6tcv: Crystal structure of Bacteroides thetaiotamicron EndoBT-3987 in c... -

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Basic information

Entry
Database: PDB / ID: 6tcv
TitleCrystal structure of Bacteroides thetaiotamicron EndoBT-3987 in complex with Man9GlcNAc2Asn substrate
ComponentsEndo-beta-N-acetylglucosaminidase F1
KeywordsHYDROLASE / endo-b-N-acetylglucosaminidase / EndoBT / glycoside hydrolase
Function / homology
Function and homology information


Domain of unknown function DUF1735 / BT_3987-like, N-terminal domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ASPARAGINE / Endo-beta-N-acetylglucosaminidase F1
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.311 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
DepositionNov 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,2424
Polymers49,1341
Non-polymers2,1083
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint44 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.495, 115.495, 97.422
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Endo-beta-N-acetylglucosaminidase F1


Mass: 49133.781 Da / Num. of mol.: 1 / Mutation: D312A, E314L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3987 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A0N4
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1883.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,11,10/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1_j2-k1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ASN / ASPARAGINE


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 00 mM M MES pH 6, 50 mM CaCl2 and 10% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.31→29.865 Å / Num. obs: 115143 / % possible obs: 99.1 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.75
Reflection shellResolution: 1.31→29.865 Å / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.33 / Num. unique obs: 10639 / CC1/2: 0.671

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Processing

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

3poh


Resolution: 1.311→29.865 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 15.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1772 5621 4.88 %
Rwork0.1587 109522 -
obs0.1596 115143 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.82 Å2 / Biso mean: 22.4451 Å2 / Biso min: 10.42 Å2
Refinement stepCycle: final / Resolution: 1.311→29.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 274 268 3490
Biso mean--25.39 28.22 -
Num. residues----397
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.311-1.32540.28781270.2582271472
1.3254-1.3410.2511940.22643609100
1.341-1.35740.21631610.21633714100
1.3574-1.37460.21291770.20293720100
1.3746-1.39270.20061990.18913697100
1.3927-1.41170.18712000.18573662100
1.4117-1.43190.19471860.1813703100
1.4319-1.45330.18512150.1713691100
1.4533-1.4760.14932060.14933618100
1.476-1.50020.17251940.15983718100
1.5002-1.52610.15351850.14783687100
1.5261-1.55380.15751980.1433680100
1.5538-1.58370.14842010.14233669100
1.5837-1.6160.15532000.14253654100
1.616-1.65110.17452030.14313680100
1.6511-1.68950.15372000.13413668100
1.6895-1.73180.14991800.13693688100
1.7318-1.77860.14761830.1413727100
1.7786-1.83090.16851800.14223700100
1.8309-1.890.15291860.13653686100
1.89-1.95760.17162200.1423666100
1.9576-2.03590.16311640.13853683100
2.0359-2.12860.14311750.14313712100
2.1286-2.24080.18692050.14543659100
2.2408-2.38110.16651640.14583717100
2.3811-2.56480.17172040.15213671100
2.5648-2.82280.18941960.15573658100
2.8228-3.23080.16451360.1618372599
3.2308-4.06890.17871900.1648368399
4.0689-29.8650.21081920.18813663100
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)
12.98560.178-0.4560.0736-0.32762.09690.0297-0.402-0.38670.23980.20490.3059-0.2569-0.2201-0.19890.24170.02540.06570.24390.0860.320222.46677.65211.7238
25.6856-0.6657-3.27641.17021.10924.6368-0.2055-0.0912-0.65210.2650.16640.6272-0.0446-0.31750.12870.1242-0.01190.01150.22130.08170.272617.21469.2919-1.2179
31.4915-0.36470.61261.1342-0.29391.08510.0243-0.204-0.16470.11150.07340.3401-0.139-0.2082-0.06710.19490.02490.05110.21350.0490.215333.5298.00371.2614
40.5675-0.11280.180.5385-0.15190.7593-0.01060.00930.0019-0.0426-0.00390.0688-0.0663-0.01620.01360.139-0.0113-0.00670.1067-0.00210.133938.600416.952-16.529
52.6929-0.66210.95671.47590.50920.7698-0.0193-0.25740.16350.09140.0343-0.1208-0.20930.1723-0.02720.2009-0.0313-0.02240.1422-0.00060.158251.219723.2265-4.7273
61.4779-0.8039-0.02341.55270.29841.8216-0.0571-0.10170.06490.06720.0456-0.09660.01420.1822-0.01630.1139-0.0243-0.00890.12620.01570.114756.728912.5346-4.2708
77.61313.05017.33693.25792.07067.4414-0.56250.15532.5326-0.6271-0.128-0.7398-2.05331.52340.72670.5461-0.1720.17320.2924-0.03470.642852.296534.3425-19.2438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 50 through 149 )B50 - 149
2X-RAY DIFFRACTION2chain 'B' and (resid 150 through 168 )B150 - 168
3X-RAY DIFFRACTION3chain 'B' and (resid 169 through 193 )B169 - 193
4X-RAY DIFFRACTION4chain 'B' and (resid 194 through 391 )B194 - 391
5X-RAY DIFFRACTION5chain 'B' and (resid 392 through 411 )B392 - 411
6X-RAY DIFFRACTION6chain 'B' and (resid 412 through 476 )B412 - 476
7X-RAY DIFFRACTION7chain 'A' and (resid 1 through 1 )A1

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