[English] 日本語
Yorodumi
- PDB-4hya: HYALURONIC ACID, THE ROLE OF DIVALENT CATIONS IN CONFORMATION AND... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 4hya
TitleHYALURONIC ACID, THE ROLE OF DIVALENT CATIONS IN CONFORMATION AND PACKING
DescriptorHYALURONIC ACID (POLY D-GLUCURONIC ACID-N-ACETYL-D-GLUCOSAMINE) HIGH HUMIDITY CALCIUM SALT
TRIGONAL FORM.
KeywordsTEXTURE OF CONNECTIVE TISSUE
MethodFiber diffraction (3 Å resolution)
AuthorsArnott, S.
CitationJ.Mol.Biol., 1977, 117, 761-784

primary. J.Mol.Biol., 1977, 117, 761-784 Yorodumi Papers
Hyaluronic acid: the role of divalent cations in conformation and packing.
Winter, W.T. / Arnott, S.

#1. Acta Crystallogr.,Sect.A, 1978, 34, 3-
Lals, a Linked-Atom Least-Squares Reciprocal-Space Refinement System Incorporating Stereochemical Restraints to Supplement Sparse Diffraction Data
Smith, P.J.C. / Arnott, S.

#2. J.Mol.Biol., 1975, 99, 219-
Hyaluronic Acid, Structure of a Fully Extended 3-Fold Helical Sodium Salt and Comparison with the Less Extended 4-Fold Helical Forms
Winter, W.T. / Smith, P.J.C. / Arnott, S.

#3. J.Mol.Biol., 1975, 95, 384-
Hyaluronic Acid, Molecular Conformations and Interactions in Two Sodium Salts
Guss, J.M. / Hukins, D.W.L. / Smith, P.J.C. / Winter, W.T. / Arnott, S. / Moorhouse, R. / Rees, D.A.

DateDeposition: Nov 20, 1977 / Release: Mar 28, 1980
RevisionDateData content typeGroupProviderType
1.0Mar 28, 1980Structure modelrepositoryInitial release
1.1Mar 21, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

-
Structure visualization

3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,3669
Polyers0
Non-polymers1,3669
Water1629
Unit cell
γ
α
β
Length a, b, c (Å)20.930, 20.930, 28.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP 32 1 2

-
Components

#1: ChemicalChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 3 / Formula: C8H15NO6
#2: ChemicalChemComp-GCU / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 3 / Formula: C6H10O7
#3: ChemicalChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Formula: Ca
#4: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: FIBER DIFFRACTION

-
Data collection

Radiation wavelengthRelative weight: 1

-
Processing

Software
NameVersionClassification
LINKED-ATOMLEAST-SQUARES MODEL-BUILDING PROCEDURErefinement
LALSrefinement
Least-squares processHighest resolution: 3 Å
Refine hist #LASTHighest resolution: 3 Å
Number of atoms included #LASTProtein: 0 / Nucleic acid: 0 / Ligand: 81 / Solvent: 9 / Total: 90
Least-squares process
*PLUS
Highest resolution: 3 Å

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

+
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more