[English] 日本語
Yorodumi
- PDB-1ojo: SPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ojo
TitleSPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE: COMPLEX OF THE TYR408PHE MUTANT WITH 4-SULPHATED CHONDROITIN DISACCHARIDE
ComponentsHYALURONATE LYASE
KeywordsLYASE / PROTEIN-CARBOHYDRATE COMPLEX
Function / homology
Function and homology information


hyaluronate lyase / hyaluronate lyase activity / : / hydrolase activity, acting on glycosyl bonds / carbohydrate binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
: / Hyaluronate lyase, N-terminal beta-sheet domain / Hyaluronate lyase, beta-sheet domain superfamily / Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain ...: / Hyaluronate lyase, N-terminal beta-sheet domain / Hyaluronate lyase, beta-sheet domain superfamily / Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Chondroitinase Ac; Chain A, domain 3 / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Glycosyltransferase / Alpha/alpha barrel / Galactose-binding-like domain superfamily / Distorted Sandwich / Immunoglobulin E-set / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRigden, D.J. / Jedrzejas, M.J.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Structures of Streptococcus Pneumoniae Hyaluronate Lyase in Complex with Chondroitin and Chondroitin Sulfate Disaccharides: Insights Into Specificity and Mechanism of Action
Authors: Rigden, D.J. / Jedrzejas, M.J.
#1: Journal: Embo J. / Year: 2000
Title: Structural Basis of Hyaluronan Degradation by Streptococcus Pneumoniae Hyaluronate Lyase
Authors: Li, S. / Kelly, S.J. / Lamani, E. / Ferraroni, M. / Jedrzejas, M.J.
History
DepositionJul 11, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2003Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HYALURONATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4906
Polymers83,6461
Non-polymers8445
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)83.739, 103.779, 101.151
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein HYALURONATE LYASE / HYALURONIDASE / HYASE


Mass: 83646.078 Da / Num. of mol.: 1 / Fragment: HYALURONATE LYASE, RESIDUES 285-1009 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q54873, hyaluronate lyase
#2: Polysaccharide 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose


Type: oligosaccharide / Mass: 459.380 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2112h-1b_1-5_2*NCC/3=O_4*OSO/3=O/3=O][a21eEA-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc4SO3]{[(3+1)][a-L-4-deoxy-IdopA]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION TYR 525 PHE
Sequence detailsTHE PROTEIN USED WAS THE Y408F MUTANT. THE SIX RESIDUE HIS TAG, ALONG WITH RESIDUES 168-169 AND ...THE PROTEIN USED WAS THE Y408F MUTANT. THE SIX RESIDUE HIS TAG, ALONG WITH RESIDUES 168-169 AND 892, WERE NOT SEEN IN THE DENSITY. THE ELECTRON DENSITY OF RESIDUE 731 SUGGESTS IT IS A VALINE THE SEQUENCE CONFLICT AT RESIDUE A196 (SWS RESIDUE 313) IS MARKED AS A KNOWN SEQUENCE CONFLICT IN THE SWS ENTRY.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.39 %
Crystal growpH: 6
Details: 3.5M AMMONIUM SULFATE, 200MM SODIUM CACODYLATE, PH 6.0
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
210 mMTris-HCl1droppH7.4
3150 mMEDTA1drop
42 mMEDTA1drop
550 mMchondroitin solution1reservoir
610 mMTris-HCl1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793
DetectorType: OXFORD / Detector: CCD / Date: Jun 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→39.96 Å / Num. obs: 63869 / % possible obs: 86.7 % / Redundancy: 7.9 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 25
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.2 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.75 Å / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.2

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C82

1c82


Resolution: 1.75→39.96 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2256586 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 4429 5 %RANDOM
Rwork0.202 ---
obs0.202 893555 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.7568 Å2 / ksol: 0.400055 e/Å3
Displacement parametersBiso mean: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1--8.3 Å20 Å20 Å2
2--1.19 Å20 Å2
3---7.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.75→39.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5798 0 50 536 6384
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.121.5
X-RAY DIFFRACTIONc_mcangle_it2.632
X-RAY DIFFRACTIONc_scbond_it3.532
X-RAY DIFFRACTIONc_scangle_it4.532.5
LS refinement shellResolution: 1.75→1.81 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.289 394 4.5 %
Rwork0.31 8413 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Num. reflection obs: 90026
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

+
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