[English] 日本語
Yorodumi
- PDB-6ojl: Structure of YePL2A R194K in Complex with Pentagalacturonic Acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ojl
TitleStructure of YePL2A R194K in Complex with Pentagalacturonic Acid
ComponentsPeriplasmic pectate lyase
KeywordsLYASE / pectin / (alpha/alpha)8
Function / homology
Function and homology information


carbon-oxygen lyase activity, acting on polysaccharides / pectin catabolic process / periplasmic space
Similarity search - Function
SH3 type barrels. - #880 / Molybdopterin biosynthesis moea protein, domain 2 - #40 / Periplasmic pectate lyase / Periplasmic pectate lyase / Molybdopterin biosynthesis moea protein, domain 2 / Glycosyltransferase - #20 / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / SH3 type barrels. ...SH3 type barrels. - #880 / Molybdopterin biosynthesis moea protein, domain 2 - #40 / Periplasmic pectate lyase / Periplasmic pectate lyase / Molybdopterin biosynthesis moea protein, domain 2 / Glycosyltransferase - #20 / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / SH3 type barrels. / Roll / Alpha-Beta Complex / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Periplasmic pectate lyase
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsJones, D.R. / Abbott, D.W.
CitationJournal: J.Struct.Biol. / Year: 2019
Title: A surrogate structural platform informed by ancestral reconstruction and resurrection of a putative carbohydrate binding module hybrid illuminates the neofunctionalization of a pectate lyase.
Authors: Jones, D.R. / McLean, R. / Hobbs, J.K. / Abbott, D.W.
History
DepositionApr 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: 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 / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: 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: Periplasmic pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3995
Polymers64,3141
Non-polymers1,0854
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.510, 96.080, 127.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Periplasmic pectate lyase


Mass: 64313.789 Da / Num. of mol.: 1 / Mutation: R194K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: pelY, ERS137951_00187 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A0T9S209
#2: Polysaccharide alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D- ...alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-beta-D-galactopyranuronic acid


Type: oligosaccharide / Mass: 898.634 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpAa1-4DGalpAa1-4DGalpAa1-4DGalpAa1-4DGalpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2112A-1b_1-5][a2112A-1a_1-5]/1-2-2-2-2/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-GalpA]{[(4+1)][a-D-GalpA]{[(4+1)][a-D-GalpA]{[(4+1)][a-D-GalpA]{[(4+1)][a-D-GalpA]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 1500, Sodium Acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.5→46.53 Å / Num. obs: 114656 / % possible obs: 99.56 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.04494 / Net I/σ(I): 17.82
Reflection shellResolution: 1.5→1.5171 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.6217 / Mean I/σ(I) obs: 2.63 / Num. unique obs: 3554 / % possible all: 99.87

-
Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v8k
Resolution: 1.5→46.507 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / Phase error: 17.59
RfactorNum. reflection% reflection
Rfree0.1862 5733 5 %
Rwork0.1681 --
obs0.1686 114656 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→46.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4279 0 73 536 4888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054586
X-RAY DIFFRACTIONf_angle_d0.7916247
X-RAY DIFFRACTIONf_dihedral_angle_d10.8612732
X-RAY DIFFRACTIONf_chiral_restr0.05657
X-RAY DIFFRACTIONf_plane_restr0.006837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51710.26261870.24223554X-RAY DIFFRACTION100
1.5171-1.53490.25361880.22843582X-RAY DIFFRACTION100
1.5349-1.55360.28221900.22183602X-RAY DIFFRACTION100
1.5536-1.57330.22611910.21153626X-RAY DIFFRACTION100
1.5733-1.5940.23041900.20783610X-RAY DIFFRACTION100
1.594-1.61580.23071890.20513602X-RAY DIFFRACTION100
1.6158-1.63890.21831880.19943563X-RAY DIFFRACTION100
1.6389-1.66340.20591930.18983677X-RAY DIFFRACTION100
1.6634-1.68940.2181890.18683579X-RAY DIFFRACTION100
1.6894-1.71710.22041910.18173627X-RAY DIFFRACTION100
1.7171-1.74670.23241890.18663600X-RAY DIFFRACTION100
1.7467-1.77840.21081910.18253617X-RAY DIFFRACTION100
1.7784-1.81260.20971900.17983614X-RAY DIFFRACTION100
1.8126-1.84960.18621910.17113627X-RAY DIFFRACTION100
1.8496-1.88990.20861900.17093616X-RAY DIFFRACTION100
1.8899-1.93380.20651900.17753604X-RAY DIFFRACTION100
1.9338-1.98220.19521910.17963622X-RAY DIFFRACTION100
1.9822-2.03580.17361910.17243632X-RAY DIFFRACTION100
2.0358-2.09570.19491920.16813653X-RAY DIFFRACTION100
2.0957-2.16330.17851920.16233641X-RAY DIFFRACTION100
2.1633-2.24070.18651910.16663631X-RAY DIFFRACTION100
2.2407-2.33040.1741910.16453642X-RAY DIFFRACTION100
2.3304-2.43640.17771920.16663648X-RAY DIFFRACTION100
2.4364-2.56490.19641920.17263643X-RAY DIFFRACTION100
2.5649-2.72550.17591910.16553621X-RAY DIFFRACTION99
2.7255-2.93590.21451940.16993683X-RAY DIFFRACTION99
2.9359-3.23130.17771920.16963651X-RAY DIFFRACTION99
3.2313-3.69880.1881930.16253673X-RAY DIFFRACTION99
3.6988-4.65940.14921930.13563672X-RAY DIFFRACTION98
4.6594-46.52920.1562010.15533805X-RAY DIFFRACTION97

+
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://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