[English] 日本語
Yorodumi
- PDB-1n7r: Streptococcus pneumoniae Hyaluronate Lyase W291A/W292A/F343V Muta... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1n7r
TitleStreptococcus pneumoniae Hyaluronate Lyase W291A/W292A/F343V Mutant complex with hexasaccharide hyaluronan
ComponentsHYALURONIDASE
KeywordsLYASE / protein mutant
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 / 2.2 Å resolution
AuthorsNukui, M. / Taylor, K.B. / McPherson, D.T. / Shigenaga, M. / Jedrzejas, M.J.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The function of hydrophobic residues in the catalytic cleft of Streptococcus pneumoniae hyaluronate lyase. Kinetic characterization of mutant enzyme forms
Authors: Nukui, M. / Taylor, K.B. / McPherson, D.T. / Shigenaga, M. / Jedrzejas, M.J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 16, 2002 / Release: Dec 31, 2002
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 31, 2002Structure modelrepositoryInitial release
1.1Apr 28, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance
1.3Oct 11, 2017Structure modelRefinement descriptionsoftware_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HYALURONIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2857
Polyers82,0391
Non-polymers1,2466
Water8,845491
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)84.491, 102.494, 103.698
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 HYALURONIDASE / / HYALURONATE LYASE


Mass: 82039.328 Da / Num. of mol.: 1 / Mutation: W291A/W292A/F343V / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Genus: Streptococcus / Plasmid name: pEt20 / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli)
References: GenBank: 437705, UniProt: Q54873*PLUS, hyaluronate lyase
#2: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


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


Mass: 194.139 Da / Num. of mol.: 3 / Formula: C6H10O7 / Glucuronic acid
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 / Density percent sol: 51.05 %
Crystal growTemp: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: AMMONIUM SULFATE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
components of the solutions
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDChemical formulaDetails
16.2 mg/mlproteindrop
260-65 %satammonium sulfatereservoir
30.2 MreservoirNaCl
42 %dioxanereservoir
550 mMsodium citratereservoirpH6.0

-
Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Details: SI / Detector: CCD / Collection date: Jul 21, 2002
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: 2.2 Å / D resolution low: 5 Å / Number obs: 45691 / Rmerge I obs: 0.206 / Rsym value: 0.206 / Redundancy: 8.6 % / Percent possible obs: 99.8
Reflection shellRmerge I obs: 0.421 / Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / Rsym value: 0.421
Reflection
*PLUS
D resolution high: 2.21 Å / D resolution low: 5 Å / Number obs: 45837 / Number measured all: 394836
Reflection shell
*PLUS
Percent possible obs: 98.2

-
Processing

Software
NameClassification
MADNESSdata collection
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
MADNESSdata reduction
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LOH
Sigma F: 0 / Sigma I: 0
Least-squares processR factor R free: 0.222 / R factor R work: 0.177 / R factor obs: 0.177 / Highest resolution: 2.2 Å / Lowest resolution: 2 Å / Number reflection R free: 897 / Number reflection obs: 45691
Refine hist #LASTHighest resolution: 2.2 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 5762 / Nucleic acid: 0 / Ligand: 79 / Solvent: 491 / Total: 6332
Least-squares process
*PLUS
Highest resolution: 2.21 Å / Lowest resolution: 5 Å
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.025
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg2.263
Refine LS shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / R factor R free: 0.285 / R factor R work: 0.204

+
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