[English] 日本語
Yorodumi
- PDB-1lxk: Streptococcus pneumoniae Hyaluronate Lyase in Complex with Tetras... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1lxk
TitleStreptococcus pneumoniae Hyaluronate Lyase in Complex with Tetrasaccharide Hyaluronan Substrate
ComponentsHyaluronate Lyase
KeywordsLYASE / PROTEIN-CARBOHYDRATE COMPLEX
Function / homologyPolysaccharide lyase family 8-like, C-terminal / Hyaluronate lyase, beta-sheet domain superfamily / Gram-positive cocci surface proteins LPxTG motif profile. / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, super-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, C-terminal / Chondroitin AC/alginate lyase / Galactose-binding-like domain superfamily ...Polysaccharide lyase family 8-like, C-terminal / Hyaluronate lyase, beta-sheet domain superfamily / Gram-positive cocci surface proteins LPxTG motif profile. / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, super-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, C-terminal / Chondroitin AC/alginate lyase / Galactose-binding-like domain superfamily / Galactose mutarotase-like domain superfamily / Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Glycoside hydrolase-type carbohydrate-binding / Immunoglobulin E-set / hyaluronate lyase / hyaluronate lyase activity / cell wall / carbohydrate binding / carbohydrate metabolic process / extracellular region / Hyaluronate lyase / gb:437705:
Function and homology information
Specimen sourceStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.53 Å resolution
AuthorsJedrzejas, M.J. / Mello, L.V. / De Groot, B.L. / Li, S.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Mechanism of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase. Structures of complexes with the substrate.
Authors: Jedrzejas, M.J. / Mello, L.V. / de Groot, B.L. / Li, S.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 5, 2002 / Release: Aug 7, 2002
RevisionDateData content typeGroupProviderType
1.0Aug 7, 2002Structure modelrepositoryInitial release
1.1Apr 28, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hyaluronate Lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1325
Polyers82,3021
Non-polymers8314
Water12,340685
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)83.736, 103.817, 101.347
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

-
Components

#1: Protein/peptide Hyaluronate Lyase / / HYALURONIDASE


Mass: 82301.641 Da / Num. of mol.: 1 / Mutation: Y408F / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Genus: Streptococcus / Plasmid name: pET21 / Genus (production host): Escherichia / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: GenBank: 437705, UniProt: Q54873*PLUS, hyaluronate lyase
#2: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 2 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 2 / Formula: C6H10O7 / Glucuronic acid
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 685 / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 / Density percent sol: 54.03 %
Crystal growTemp: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: AMMONIUM SULFATE, SODIUM Cacodylate, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temp: 22 ℃ / pH: 7.4
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDDetails
15 mg/mlenzyme1drop
210 mMTris-HCl1droppH7.4
32 mMEDTA1drop
41 mMDL-dithiothreitol1drop
5100 mMsodium cacodylate1reservoirpH6.0
62.9 Mammonium sulfate1reservoir
75 mMEDTA1reservoir

-
Data collection

DiffractionMean temperature: 298 kelvins
SourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1
DetectorType: OXFORD / Detector: CCD / Collection date: Mar 20, 2001
RadiationMonochromator: SI / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionD resolution high: 1.53 Å / D resolution low: 5 Å / Number obs: 124799 / Percent possible obs: 93.1
Reflection shellHighest resolution: 1.53 Å / Lowest resolution: 1.58 Å / Percent possible all: 49.8
Reflection
*PLUS
D resolution high: 1.52 Å / D resolution low: 5 Å / Number obs: 124927 / Number measured all: 904361 / Rmerge I obs: 0.08
Reflection shell
*PLUS
Highest resolution: 1.52 Å / Lowest resolution: 1.59 Å / Percent possible obs: 49.8 / Rmerge I obs: 0.611

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
HKL-2000data reduction
SCALEPACKdata scaling
X-PLORphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT / R Free selection details: 1 % REFS SELECTED / Sigma F: 2
Least-squares processR factor R free: 0.239 / R factor R work: 0.19 / R factor all: 0.19 / R factor obs: 0.19 / Highest resolution: 1.53 Å / Lowest resolution: 2 Å / Number reflection R free: 1208 / Number reflection obs: 122074
Refine hist #LASTHighest resolution: 1.53 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 5774 / Nucleic acid: 0 / Ligand: 53 / Solvent: 685 / Total: 6512
Least-squares process
*PLUS
R factor R work: 0.19 / Highest resolution: 1.52 Å / Lowest resolution: 5 Å / Percent reflection R free: 1
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.235
Refine LS shell
*PLUS
Highest resolution: 1.52 Å / Lowest resolution: 1.59 Å / R factor R free: 0.395 / R factor R work: 0.33

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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