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- PDB-5olr: Rhamnogalacturonan lyase -

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Basic information

Entry
Database: PDB / ID: 5olr
TitleRhamnogalacturonan lyase
ComponentsRhamnogalacturonan lyase
KeywordsLYASE / Pectin / PL9 / polysaccharide lyase family 9 / Rhamnogalacturonan lyase / endo-acting enzyme
Function / homology
Function and homology information


carbon-oxygen lyase activity, acting on polysaccharides / alpha-galactosidase activity / extracellular region / metal ion binding
Similarity search - Function
Domain of unknown function DUF4990 / Rhamnogalacturonan lyase BT_4170-like, C-terminal / : / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / PHOSPHATE ION / DUF4990 domain-containing protein / Pectate lyase L
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.07 Å
AuthorsBasle, A. / Luis, A.S. / Gilbert, H.J.
CitationJournal: Nat Microbiol / Year: 2018
Title: Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides.
Authors: Luis, A.S. / Briggs, J. / Zhang, X. / Farnell, B. / Ndeh, D. / Labourel, A. / Basle, A. / Cartmell, A. / Terrapon, N. / Stott, K. / Lowe, E.C. / McLean, R. / Shearer, K. / Schuckel, J. / ...Authors: Luis, A.S. / Briggs, J. / Zhang, X. / Farnell, B. / Ndeh, D. / Labourel, A. / Basle, A. / Cartmell, A. / Terrapon, N. / Stott, K. / Lowe, E.C. / McLean, R. / Shearer, K. / Schuckel, J. / Venditto, I. / Ralet, M.C. / Henrissat, B. / Martens, E.C. / Mosimann, S.C. / Abbott, D.W. / Gilbert, H.J.
History
DepositionJul 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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 / 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.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_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_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / 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: Rhamnogalacturonan lyase
B: Rhamnogalacturonan lyase
C: Rhamnogalacturonan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,07616
Polymers170,9413
Non-polymers2,13513
Water31,6521757
1
A: Rhamnogalacturonan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7926
Polymers56,9801
Non-polymers8125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rhamnogalacturonan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6425
Polymers56,9801
Non-polymers6624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Rhamnogalacturonan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6425
Polymers56,9801
Non-polymers6624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.458, 123.872, 137.628
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein Rhamnogalacturonan lyase


Mass: 56980.395 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: HMPREF2534_01516 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A139KMS2, UniProt: Q8A051*PLUS
#2: Polysaccharide alpha-L-rhamnopyranose-(1-4)-alpha-D-galactopyranuronic acid-(1-2)-alpha-L-rhamnopyranose


Type: oligosaccharide / Mass: 486.421 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LRhapa1-4DGalpAa1-2LRhapa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2211m-1a_1-5][a2112A-1a_1-5]/1-2-1/a2-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-L-Rhap]{[(2+1)][a-D-GalpA]{[(4+1)][a-L-Rhap]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 1767 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1757 / 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: 1.93 Å3/Da / Density % sol: 36.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM succinic acid, sodium phosphate glycine buffer pH 6.0 and 25 % (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.07→48.4 Å / Num. obs: 536956 / % possible obs: 94.3 % / Redundancy: 3.2 % / CC1/2: 0.998 / Net I/σ(I): 11.3
Reflection shellResolution: 1.07→1.09 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 9262 / CC1/2: 0.378 / % possible all: 33.1

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Processing

Software
NameClassification
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
Cootmodel building
RefinementResolution: 1.07→48.4 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.047 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.028 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16643 26889 5 %RANDOM
Rwork0.1447 ---
obs0.1458 509939 94.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.582 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0 Å2
2---0.31 Å20 Å2
3---0.2 Å2
Refinement stepCycle: 1 / Resolution: 1.07→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9788 0 126 1757 11671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910432
X-RAY DIFFRACTIONr_bond_other_d0.0020.029219
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.95214190
X-RAY DIFFRACTIONr_angle_other_deg1.079321561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21751362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.51624.95505
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.866151678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8611545
X-RAY DIFFRACTIONr_chiral_restr0.0990.21534
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111882
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022119
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_it0.9610.9255191
X-RAY DIFFRACTIONr_mcbond_other0.9560.9255190
X-RAY DIFFRACTIONr_mcangle_it1.1891.3996506
X-RAY DIFFRACTIONr_mcangle_other1.191.3996507
X-RAY DIFFRACTIONr_scbond_it1.5151.1275241
X-RAY DIFFRACTIONr_scbond_other1.511.1275241
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8221.6187640
X-RAY DIFFRACTIONr_long_range_B_refined3.44313.30912122
X-RAY DIFFRACTIONr_long_range_B_other3.44313.3112123
X-RAY DIFFRACTIONr_rigid_bond_restr4.915319649
X-RAY DIFFRACTIONr_sphericity_free23.03951098
X-RAY DIFFRACTIONr_sphericity_bonded7.352520039
LS refinement shellResolution: 1.075→1.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 839 -
Rwork0.305 16400 -
obs--41.21 %

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