[English] 日本語
Yorodumi
- PDB-1ax1: ERYTHRINA CORALLODENDRON LECTIN IN COMPLEX WITH LACTOSE -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1ax1
TitleERYTHRINA CORALLODENDRON LECTIN IN COMPLEX WITH LACTOSE
ComponentsLECTIN
KeywordsLECTIN / GLYCOPROTEIN
Function / homologyLegume lectin, alpha chain, conserved site / Legume lectin domain / Concanavalin A-like lectin/glucanase domain superfamily / Legume lectin / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Legume lectins beta-chain signature. / Legume lectins alpha-chain signature. / carbohydrate binding / Lectin
Function and homology information
Specimen sourceErythrina corallodendron (coral tree)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER FROM PREVIOUSLY DETERMINED, RELATED STRUCTURE / 1.95 Å resolution
AuthorsShaanan, B. / Elgavish, S.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Structures of the Erythrina corallodendron lectin and of its complexes with mono- and disaccharides.
Authors: Elgavish, S. / Shaanan, B.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 24, 1997 / Release: May 6, 1998
RevisionDateData content typeGroupProviderType
1.0May 6, 1998Structure modelrepositoryInitial release
1.1Mar 24, 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: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,97412
Polyers26,2211
Non-polymers1,75211
Water2,666148
1
A: LECTIN
hetero molecules

A: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,94724
Polyers52,4422
Non-polymers3,50522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
γ
α
β
Length a, b, c (Å)84.060, 72.970, 71.240
Angle α, β, γ (deg.)90.00, 113.39, 90.00
Int Tables number5
Space group name H-MC 1 2 1

-
Components

-
Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide LECTIN /


Mass: 26221.180 Da / Num. of mol.: 1 / Source: (natural) Erythrina corallodendron (coral tree) / Genus: Erythrina / References: UniProt: P16404

-
Non-polymers , 10 types, 159 molecules

#2: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 2 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical ChemComp-FUC / ALPHA-L-FUCOSE


Mass: 164.156 Da / Num. of mol.: 1 / Formula: C6H12O5
#4: Chemical ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 1 / Formula: C6H12O6
#5: Chemical ChemComp-XYP / BETA-D-XYLOPYRANOSE


Mass: 150.130 Da / Num. of mol.: 1 / Formula: C5H10O5
#6: Chemical ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 2 / Formula: C6H12O6
#7: Chemical ChemComp-BGC / BETA-D-GLUCOSE


Mass: 180.156 Da / Num. of mol.: 1 / Formula: C6H12O6 / Glucose
#8: Chemical ChemComp-GAL / BETA-D-GALACTOSE


Mass: 180.156 Da / Num. of mol.: 1 / Formula: C6H12O6 / Galactose
#9: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Formula: Mn / Manganese
#10: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Formula: Ca / Calcium
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.82 / Density percent sol: 67.81 %
Crystal growpH: 7 / Details: pH 7.
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
16 mg/mlprotein1drop
215 %(v/v)MPD1drop
350 mMHEPES1drop
40.02 %(w/v)sodium azide1drop
530 %MPD1reservoir
6100 mMHEPES1reservoir
70.02 %sodium azide1reservoir

-
Data collection

DiffractionMean temperature: 298 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Details: FRANCKS MIRRORS (SUPPER 2 X 6 CM MIRRORS) / Detector: IMAGE PLATE / Collection date: Jun 1, 1993
RadiationMonochromator: NI FILTER / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 30.8 Å2 / D resolution high: 1.95 Å / D resolution low: 2 Å / Number obs: 27823 / Rmerge I obs: 0.056 / Rsym value: 0.056 / NetI over sigmaI: 12 / Redundancy: 2.2 % / Percent possible obs: 91.4
Reflection shellRmerge I obs: 0.056 / Highest resolution: 1.95 Å / Lowest resolution: 2.04 Å / MeanI over sigI obs: 5 / Rsym value: 0.263 / Redundancy: 2 % / Percent possible all: 91
Reflection
*PLUS
Number measured all: 60388
Reflection shell
*PLUS
Rmerge I obs: 0.263

+
Processing

Software
NameVersionClassification
X-PLORmodel building
CNS0.1refinement
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefineMethod to determine structure: DIFFERENCE FOURIER FROM PREVIOUSLY DETERMINED, RELATED STRUCTURE
Starting model: COMPLEX WITH LACTOSE, PDB ENTRY 1LTE
R Free selection details: RANDOM / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Displacement parametersB iso mean: 32.4 Å2 / Aniso B11: -2.47 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0.06 Å2 / Aniso B22: 3 Å2 / Aniso B23: 0 Å2 / Aniso B33: -0.52 Å2
Least-squares processR factor R free: 0.2 / R factor R free error: 0.003 / R factor R work: 0.173 / R factor obs: 0.173 / Highest resolution: 1.95 Å / Lowest resolution: 6 Å / Number reflection R free: 2583 / Number reflection obs: 26067 / Percent reflection R free: 9.9 / Percent reflection obs: 93.4
Refine analyzeLuzzati coordinate error free: 0.21 Å / Luzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.25 Å / Luzzati sigma a obs: 0.25 Å
Refine hist #LASTHighest resolution: 1.95 Å / Lowest resolution: 6 Å
Number of atoms included #LASTProtein: 1855 / Nucleic acid: 0 / Ligand: 105 / Solvent: 148 / Total: 2108
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.25
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.541.50
X-RAY DIFFRACTIONc_mcangle_it2.442.00
X-RAY DIFFRACTIONc_scbond_it3.282.00
X-RAY DIFFRACTIONc_scangle_it4.812.50
Refine LS shellHighest resolution: 1.95 Å / R factor R free: 0.301 / R factor R free error: 0.019 / R factor R work: 0.321 / Lowest resolution: 2.02 Å / Number reflection R free: 246 / Number reflection R work: 2282 / Total number of bins used: 10 / Percent reflection R free: 9.7 / Percent reflection obs: 91.4
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: CNS / Version: 0.1 / Classification: refinement
Least-squares process
*PLUS
R factor R free: 0.2
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.25

+
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