[English] 日本語
Yorodumi
- PDB-7o84: Structure of the PL6 family alginate lyase Pedsa0632 from Pseudop... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7o84
TitleStructure of the PL6 family alginate lyase Pedsa0632 from Pseudopedobacter saltans in complex with substrate
ComponentsAlginate lyase
KeywordsLYASE / beta helix
Function / homology
Function and homology information


PL-6 family / Chondroitinase B / Parallel beta-helix repeat / Parallel beta-helix repeats / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Beta
Similarity search - Domain/homology
Poly(Beta-D-mannuronate) lyase
Similarity search - Component
Biological speciesPseudopedobacter saltans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.177 Å
AuthorsBallut, L. / Violot, S. / Carrique, L. / Aghajari, N.
CitationJournal: Glycobiology / Year: 2021
Title: Exploring molecular determinants of polysaccharide lyase family 6-1 enzyme activity.
Authors: Violot, S. / Galisson, F. / Carrique, L. / Jugnarain, V. / Conchou, L. / Robert, X. / Thureau, A. / Helbert, W. / Aghajari, N. / Ballut, L.
History
DepositionApr 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Data collection / Database references
Category: citation / database_2 / pdbx_entity_branch_descriptor
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alginate lyase
B: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1334
Polymers94,9002
Non-polymers1,2332
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint21 kcal/mol
Surface area29760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.182, 47.583, 116.200
Angle α, β, γ (deg.)90.000, 98.250, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Alginate lyase


Mass: 47450.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudopedobacter saltans (strain ATCC 51119 / DSM 12145 / JCM 21818 / LMG 10337 / NBRC 100064 / NCIMB 13643) (bacteria)
Strain: ATCC 51119 / DSM 12145 / JCM 21818 / LMG 10337 / NBRC 100064 / NCIMB 13643
Gene: Pedsa_0632 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F0S7Y7
#2: Polysaccharide 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L- ...4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid


Type: oligosaccharide / Mass: 528.372 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a1121A-1a_1-5][a11eEA-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-L-GulpA]{[(4+1)][a-L-GulpA]{[(4+1)][b-D-4-deoxy-ManpA]{}}}LINUCSPDB-CARE
#3: Polysaccharide 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L- ...4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid


Type: oligosaccharide / Mass: 704.495 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,3/[a1121A-1a_1-5][a11eEA-1a_1-5]/1-1-1-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-L-GulpA]{[(4+1)][a-L-GulpA]{[(4+1)][a-L-GulpA]{[(4+1)][b-D-4-deoxy-ManpA]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Amm chloride, 20% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 2.17→47.58 Å / Num. obs: 46036 / % possible obs: 97.8 % / Redundancy: 3.3 % / CC1/2: 0.99 / Net I/σ(I): 4.8
Reflection shellResolution: 2.17→2.31 Å / Num. unique obs: 7197 / CC1/2: 0.43

-
Processing

Software
NameVersionClassification
BUSTER2.10.3 (29-NOV-2019)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: native Pedsa0632

Resolution: 2.177→43.97 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.874 / SU R Cruickshank DPI: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.305 / SU Rfree Blow DPI: 0.239 / SU Rfree Cruickshank DPI: 0.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2862 2282 4.98 %RANDOM
Rwork0.2284 ---
obs0.2312 45831 98.3 %-
Displacement parametersBiso max: 78.09 Å2 / Biso mean: 40.9879 Å2 / Biso min: 21.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.0576 Å20 Å2-1.9927 Å2
2---8.1966 Å20 Å2
3---7.139 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 2.177→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6293 0 84 372 6749
Biso mean--64.43 41.37 -
Num. residues----817
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2231SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1139HARMONIC5
X-RAY DIFFRACTIONt_it6520HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion877SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5489SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6520HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg8849HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion3.49
X-RAY DIFFRACTIONt_other_torsion18.71
LS refinement shellResolution: 2.18→2.2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2619 52 5.67 %
Rwork0.2257 865 -
all0.2278 917 -
obs--72.37 %

+
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