[English] 日本語
Yorodumi
- PDB-5ols: Rhamnogalacturonan lyase -

+
Open data


ID or keywords:

Loading...

-
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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity % sol: 34.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200 mM potassium chloride and 20% PEG 3350

-
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

-
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 °

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more