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- PDB-5ols: Rhamnogalacturonan lyase -

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Basic information

Entry
Database: PDB / ID: 5ols
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 / : / Pel9A-like, right handed beta helix region / : / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
DUF4990 domain-containing protein / Pectate lyase L
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / 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 / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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 2.1Jan 17, 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
A: Rhamnogalacturonan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0455
Polymers56,9801
Non-polymers1,0654
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-11 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.420, 76.600, 122.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Rhamnogalacturonan lyase


Mass: 56980.395 Da / Num. of mol.: 1
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.: 1
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
#3: Polysaccharide 4-deoxy-beta-L-threo-hex-4-enopyranuronic acid-(1-2)-alpha-L-rhamnopyranose-(1-4)-beta-D- ...4-deoxy-beta-L-threo-hex-4-enopyranuronic acid-(1-2)-alpha-L-rhamnopyranose-(1-4)-beta-D-galactopyranuronic acid


Type: oligosaccharide / Mass: 498.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a2112A-1b_1-5][a2211m-1a_1-5][a21eEA-1b_1-5]/1-2-3/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-GalpA]{[(4+1)][b-L-Rhap]{[(2+1)][a-D-4-deoxy-GlcpA]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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 % sol: 34.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200 mM potassium chloride and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97912 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.2→61.7 Å / Num. obs: 22486 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 0.998 / Net I/σ(I): 13.4
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1650 / CC1/2: 0.553 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OLQ

5olq


Resolution: 2.2→61.38 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 25.522 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R: 0.338 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27105 1182 5.3 %RANDOM
Rwork0.233 ---
obs0.23506 21253 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.136 Å2
Baniso -1Baniso -2Baniso -3
1--2.56 Å2-0 Å20 Å2
2--2.03 Å2-0 Å2
3---0.53 Å2
Refinement stepCycle: 1 / Resolution: 2.2→61.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3257 0 69 3 3329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193403
X-RAY DIFFRACTIONr_bond_other_d0.0020.022964
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9624621
X-RAY DIFFRACTIONr_angle_other_deg0.9336917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3115424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.58124.938162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22815523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4951514
X-RAY DIFFRACTIONr_chiral_restr0.1720.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213837
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02684
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_it0.3662.1171699
X-RAY DIFFRACTIONr_mcbond_other0.3652.1171698
X-RAY DIFFRACTIONr_mcangle_it0.6263.1752122
X-RAY DIFFRACTIONr_mcangle_other0.6263.1752123
X-RAY DIFFRACTIONr_scbond_it0.4072.2171704
X-RAY DIFFRACTIONr_scbond_other0.4072.2181705
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.6063.3232500
X-RAY DIFFRACTIONr_long_range_B_refined2.00125.1773579
X-RAY DIFFRACTIONr_long_range_B_other2.00125.1873580
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 91 -
Rwork0.385 1553 -
obs--99.46 %
Refinement TLS params.Method: refined / Origin x: -4.586 Å / Origin y: 21.187 Å / Origin z: -25.988 Å
111213212223313233
T0.3246 Å2-0.0058 Å20.038 Å2-0.2514 Å20.0923 Å2--0.0872 Å2
L2.8231 °2-0.2399 °22.462 °2-6.3957 °2-0.102 °2--3.7563 °2
S-0.1122 Å °0.7357 Å °0.0851 Å °0.3685 Å °0.3316 Å °0.3886 Å °-0.0049 Å °0.4126 Å °-0.2194 Å °

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