[English] 日本語
Yorodumi
- PDB-8r72: Polysaccharide lyase BtPL33HA (BT4410) Y291A with HA dp4 collecte... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8r72
TitlePolysaccharide lyase BtPL33HA (BT4410) Y291A with HA dp4 collected at 1.33 A
ComponentsHeparinase
KeywordsLYASE / Polysaccharide lyase / glycosaminoglycan / Hyaluronic acid / conformational change
Function / homologyHeparinase II/III-like / Heparinase II/III-like, C-terminal / Chondroitin AC/alginate lyase / cell envelope / lyase activity / metal ion binding / Heparinase II/III-like C-terminal domain-containing protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsCartmell, A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Royal Society212050 United Kingdom
Wellcome Trust1065163470 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Bacterial polysaccharide lyase family 33: Specificity from an evolutionarily conserved binding tunnel.
Authors: Loiodice, M. / Drula, E. / McIver, Z. / Antonyuk, S. / Basle, A. / Lima, M. / Yates, E.A. / Byrne, D.P. / Coughlan, J. / Leech, A. / Mesdaghi, S. / Rigden, D.J. / Drouillard, S. / Helbert, W. ...Authors: Loiodice, M. / Drula, E. / McIver, Z. / Antonyuk, S. / Basle, A. / Lima, M. / Yates, E.A. / Byrne, D.P. / Coughlan, J. / Leech, A. / Mesdaghi, S. / Rigden, D.J. / Drouillard, S. / Helbert, W. / Henrissat, B. / Terrapon, N. / Wright, G.S.A. / Couturier, M. / Cartmell, A.
History
DepositionNov 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heparinase
B: Heparinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,8216
Polymers147,1372
Non-polymers1,6844
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-65 kcal/mol
Surface area46800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.870, 137.400, 203.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Heparinase


Mass: 73568.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_4410 / Production host: Escherichia coli (E. coli) / References: UniProt: Q89ZG7
#2: Polysaccharide beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 776.648 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpAb1-3DGlcpNAcb1-4DGlcpAb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2122A-1b_1-5]/1-2-1-2/a3-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 20 % PEG 6000 0.1 M MES pH 6.0 0.1 M Ammonium chloride 20 mg/ml

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.33 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.33 Å / Relative weight: 1
ReflectionResolution: 2.58→53.87 Å / Num. obs: 48609 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.989 / Net I/σ(I): 8.4
Reflection shellResolution: 2.58→2.66 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4374 / CC1/2: 0.574

-
Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→52.128 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.884 / SU B: 14.912 / SU ML: 0.308 / Cross valid method: FREE R-VALUE / ESU R: 0.723 / ESU R Free: 0.343
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2807 2536 5.225 %
Rwork0.2186 46000 -
all0.222 --
obs-48536 99.938 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.173 Å2
Baniso -1Baniso -2Baniso -3
1-3.395 Å20 Å20 Å2
2---1.385 Å2-0 Å2
3----2.01 Å2
Refinement stepCycle: LAST / Resolution: 2.58→52.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9821 0 108 6 9935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01210172
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169449
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.67413783
X-RAY DIFFRACTIONr_angle_other_deg0.4791.59321767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.68851219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.255553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.712101752
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.98310487
X-RAY DIFFRACTIONr_chiral_restr0.0650.21471
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212043
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022429
X-RAY DIFFRACTIONr_nbd_refined0.2270.22064
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.28736
X-RAY DIFFRACTIONr_nbtor_refined0.1850.24946
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.25409
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2216
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0670.23
X-RAY DIFFRACTIONr_metal_ion_refined0.1310.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.20.219
X-RAY DIFFRACTIONr_nbd_other0.2420.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1550.23
X-RAY DIFFRACTIONr_mcbond_it3.9454.6824885
X-RAY DIFFRACTIONr_mcbond_other3.9444.6824885
X-RAY DIFFRACTIONr_mcangle_it5.9858.4136101
X-RAY DIFFRACTIONr_mcangle_other5.9848.4136102
X-RAY DIFFRACTIONr_scbond_it4.1075.0135287
X-RAY DIFFRACTIONr_scbond_other4.1075.015284
X-RAY DIFFRACTIONr_scangle_it6.3699.0917682
X-RAY DIFFRACTIONr_scangle_other6.3699.097681
X-RAY DIFFRACTIONr_lrange_it8.15345.18811350
X-RAY DIFFRACTIONr_lrange_other8.15345.19211351
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.58-2.6470.451800.34933290.35435090.8680.9221000.345
2.647-2.7190.3971810.31632590.3234400.9210.941000.306
2.719-2.7980.3621610.29631810.29933430.9220.94799.97010.285
2.798-2.8840.3381850.27230790.27532640.9280.951000.257
2.884-2.9780.2961320.2630130.26231470.9380.95499.93640.245
2.978-3.0820.3111730.24328870.24730610.9310.95999.96730.226
3.082-3.1980.3331700.24128050.24629760.9320.9699.96640.223
3.198-3.3280.3181410.24626930.2528340.9330.9591000.231
3.328-3.4750.3151360.26425900.26627260.9190.9471000.245
3.475-3.6440.291340.23825120.24126480.9450.96799.92450.223
3.644-3.840.2831400.21923730.22325160.9510.97199.88080.206
3.84-4.0720.2441130.19522420.19723560.9670.97699.95760.184
4.072-4.3510.2311290.16720980.17122290.9710.9899.91030.158
4.351-4.6970.2461040.14819840.15220930.9550.98299.76110.142
4.697-5.1410.2381000.1618500.16419520.9730.98499.89750.158
5.141-5.7410.2531070.19516590.19917680.9660.98199.88690.191
5.741-6.6160.284960.22914910.23215880.9210.95799.9370.217
6.616-8.070.206840.16812630.1713470.9750.9831000.175
8.07-11.2790.167400.1410460.14210860.9850.9871000.159
11.279-52.1280.265300.2566460.2576760.9450.9581000.277

+
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