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- PDB-6t8k: Crystal structure of Bacteroides thetaiotamicron EndoBT-3987 in c... -

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Basic information

Entry
Database: PDB / ID: 6t8k
TitleCrystal structure of Bacteroides thetaiotamicron EndoBT-3987 in complex with Man9GlcNAc product in P1
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: 2 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
A: Endo-beta-N-acetylglucosaminidase F1
B: Endo-beta-N-acetylglucosaminidase F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8296
Polymers98,3872
Non-polymers3,4414
Water9,134507
1
A: Endo-beta-N-acetylglucosaminidase F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9143
Polymers49,1941
Non-polymers1,7212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-beta-N-acetylglucosaminidase F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9143
Polymers49,1941
Non-polymers1,7212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.898, 59.633, 76.061
Angle α, β, γ (deg.)97.310, 90.140, 92.290
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 49193.746 Da / Num. of mol.: 2
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: 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


Type: oligosaccharide / Mass: 1680.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-3-3-3-3-3-3-3-3/a4-b1_b3-c1_b6-f1_c2-d1_d2-e1_f3-g1_f6-i1_g2-h1_i2-j1WURCSPDB2Glycan 1.1.0
[][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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.02 M sodium/potassium phosphate, 100 mM SPG (succinic acid, phosphate, glycine) system pH 9.0, and 25% (w/v) PEG 1500.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2→29.28 Å / Num. obs: 53616 / % possible obs: 93.27 % / Redundancy: 1.8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.054 / Net I/σ(I): 9.89
Reflection shellResolution: 2→29.28 Å / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 3.75 / Num. unique obs: 3567 / CC1/2: 0.775

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Processing

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

3poh


Resolution: 2→29.276 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 20.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1966 2419 4.7 %
Rwork0.1618 49058 -
obs0.1634 51477 93.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.18 Å2 / Biso mean: 21.3394 Å2 / Biso min: 7.61 Å2
Refinement stepCycle: final / Resolution: 2→29.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6536 0 230 507 7273
Biso mean--23.65 24.77 -
Num. residues----860
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.04080.2435950.1935185860
2.0408-2.08520.25971120.1893223674
2.0852-2.13370.23111520.1813282289
2.1337-2.1870.25461500.1829291895
2.187-2.24610.23731320.1815299897
2.2461-2.31220.23591220.1814297496
2.3122-2.38680.2271480.1754300996
2.3868-2.47210.23061530.1756302797
2.4721-2.5710.20981540.1807298797
2.571-2.68790.21481600.1677298398
2.6879-2.82950.22411180.1691304097
2.8295-3.00660.20751560.1724303598
3.0066-3.23850.1891520.1626300997
3.2385-3.56390.16721540.1549302798
3.5639-4.07840.18231590.139302298
4.0784-5.13390.14951460.1319305999
5.1339-29.2760.16031560.1551305499
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)
13.66130.0903-0.50891.1818-0.10741.92320.01550.14140.08510.01720.0113-0.0684-0.11930.0976-0.03040.2199-0.0020.00540.0992-0.01650.111434.8097-3.604325.5322
23.57432.0793-1.09223.1203-2.10832.74650.1155-0.16850.12310.1276-0.21260.0219-0.08720.22020.10250.2140.00970.0190.1055-0.03240.150733.7456-3.669930.9998
31.4189-0.19810.74720.3178-0.19331.35620.0145-0.012-0.04630.05430.00870.0290.012-0.0819-0.02040.12630.00550.02480.0915-0.00010.097116.8892-29.447626.6286
40.6043-0.1504-0.1250.5359-0.14650.8884-0.00910.03560.02790.0030.01070.007-0.0023-0.0466-0.00180.13380.00690.01030.1149-0.00260.135219.3887-26.455519.8351
53.26970.5790.49532.12790.30521.77420.10150.1465-0.2549-0.0408-0.03440.09690.2409-0.241-0.05590.2771-0.0502-0.05350.1590.02420.219113.7949-43.7104-14.1118
60.8327-0.16270.06940.46770.06780.91610.0140.0028-0.01080.0094-0.0055-0.01030.01580.0872-0.00840.1098-0.00660.00830.08540.01360.117928.6179-19.0243-15.6169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 103 )A46 - 103
2X-RAY DIFFRACTION2chain 'A' and (resid 104 through 179 )A104 - 179
3X-RAY DIFFRACTION3chain 'A' and (resid 180 through 253 )A180 - 253
4X-RAY DIFFRACTION4chain 'A' and (resid 254 through 476 )A254 - 476
5X-RAY DIFFRACTION5chain 'B' and (resid 48 through 179 )B48 - 179
6X-RAY DIFFRACTION6chain 'B' and (resid 180 through 476 )B180 - 476

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