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- PDB-3zmr: Bacteroides ovatus GH5 xyloglucanase in complex with a XXXG hepta... -

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Entry
Database: PDB / ID: 3zmr
TitleBacteroides ovatus GH5 xyloglucanase in complex with a XXXG heptasaccharide
ComponentsCELLULASE (GLYCOSYL HYDROLASE FAMILY 5)
KeywordsHYDROLASE / XYLOGLUCAN
Function / homology
Function and homology information


symbiotic process benefiting host / xyloglucan-specific endo-beta-1,4-glucanase / xyloglucan-specific endo-beta-1,4-glucanase activity / xyloglucan catabolic process / cell outer membrane
Similarity search - Function
Putative binding domain, N-terminal / Bacteroidetes-Associated Carbohydrate-binding Often N-terminal / : / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel ...Putative binding domain, N-terminal / Bacteroidetes-Associated Carbohydrate-binding Often N-terminal / : / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-D-glucopyranose / Xyloglucan-specific endo-beta-1,4-glucanase BoGH5A
Similarity search - Component
Biological speciesBACTEROIDES OVATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsLarsbrink, J. / Rogers, T.E. / Hemsworth, G.R. / McKee, L.S. / Spadiut, O. / Klinter, S. / Pudlo, N.A. / Urs, K. / Kelly, A.G. / Cederholm, S.N. ...Larsbrink, J. / Rogers, T.E. / Hemsworth, G.R. / McKee, L.S. / Spadiut, O. / Klinter, S. / Pudlo, N.A. / Urs, K. / Kelly, A.G. / Cederholm, S.N. / Davies, G.J. / Martens, E.C. / Brumer, H.
CitationJournal: Nature / Year: 2014
Title: A Discrete Genetic Locus Confers Xyloglucan Metabolism in Select Human Gut Bacteroidetes
Authors: Larsbrink, J. / Rogers, T.E. / Hemsworth, G.R. / Mckee, L.S. / Tauzin, A.S. / Spadiut, O. / Klinter, S. / Pudlo, N.A. / Urs, K. / Koropatkin, N.M. / Creagh, A.L. / Haynes, C.A. / Kelly, A.G. ...Authors: Larsbrink, J. / Rogers, T.E. / Hemsworth, G.R. / Mckee, L.S. / Tauzin, A.S. / Spadiut, O. / Klinter, S. / Pudlo, N.A. / Urs, K. / Koropatkin, N.M. / Creagh, A.L. / Haynes, C.A. / Kelly, A.G. / Cederholm, S.N. / Davies, G.J. / Martens, E.C. / Brumer, H.
History
DepositionFeb 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Mar 5, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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_alt_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 / _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.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_alt_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 / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELLULASE (GLYCOSYL HYDROLASE FAMILY 5)
B: CELLULASE (GLYCOSYL HYDROLASE FAMILY 5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,23720
Polymers105,8532
Non-polymers3,38418
Water24,1581341
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A: CELLULASE (GLYCOSYL HYDROLASE FAMILY 5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,81311
Polymers52,9271
Non-polymers1,88710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CELLULASE (GLYCOSYL HYDROLASE FAMILY 5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4249
Polymers52,9271
Non-polymers1,4978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.830, 147.240, 84.140
Angle α, β, γ (deg.)90.00, 92.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CELLULASE (GLYCOSYL HYDROLASE FAMILY 5) / XYLOGLUCANASE


Mass: 52926.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES OVATUS (bacteria) / Plasmid: PET-21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A7LXT7, xyloglucan-specific endo-beta-1,4-glucanase

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Sugars , 3 types, 3 molecules

#2: Polysaccharide alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1062.923 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DXylpa1-6]DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5][a212h-1a_1-5]/1-1-1-1-2-2-2/a4-b1_b4-c1_b6-g1_c4-d1_c6-f1_d6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-D-glucose


Type: oligosaccharide / Mass: 1062.923 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,7,6/[o2122h][a2122h-1b_1-5][a212h-1a_1-5]/1-2-2-2-3-3-3/a4-b1_b4-c1_b6-g1_c4-d1_c6-f1_d6-e1WURCSPDB2Glycan 1.1.0
[][<C6O5>]{[(1+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 1356 molecules

#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1341 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsB. OVATUS SIGNAL PEPTIDE REMOVED FOR EXPRESSION

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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: 2.85 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M BIS-TRIS PH 6.5, 20% W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 5,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.43→72.99 Å / Num. obs: 207943 / % possible obs: 99.5 % / Observed criterion σ(I): 6 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.2
Reflection shellResolution: 1.43→1.47 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JEP

2jep


Resolution: 1.43→72.99 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.807 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.15722 10458 5 %RANDOM
Rwork0.12232 ---
obs0.1241 197432 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.606 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0.44 Å2
2--0.36 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.43→72.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7267 0 224 1341 8832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197780
X-RAY DIFFRACTIONr_bond_other_d0.0010.027155
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.95710617
X-RAY DIFFRACTIONr_angle_other_deg0.903316440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3165971
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71725.026386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.033151201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8551538
X-RAY DIFFRACTIONr_chiral_restr0.090.21205
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028905
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021819
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr10.993314907
X-RAY DIFFRACTIONr_sphericity_free35.295353
X-RAY DIFFRACTIONr_sphericity_bonded41.449515713
LS refinement shellResolution: 1.43→1.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 767 -
Rwork0.216 14650 -
obs--99.75 %

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