[English] 日本語
Yorodumi
- PDB-5mxc: Aleuria aurantia lectin (AAL) N224Q mutant in complex with alpha-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mxc
TitleAleuria aurantia lectin (AAL) N224Q mutant in complex with alpha-methyl-L-fucoside
ComponentsFucose-specific lectin
KeywordsSUGAR BINDING PROTEIN / lectin / six-bladed beta-propeller / alpha-methyl fucoside
Function / homology
Function and homology information


reproductive fruiting body development / fucose binding / defense response to fungus / carbohydrate binding / protein homodimerization activity / identical protein binding
Similarity search - Function
Fucose-specific lectin / Fucose-specific lectin / Fungal fucose-specific lectin / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
methyl alpha-L-fucopyranoside / Fucose-specific lectin
Similarity search - Component
Biological speciesAleuria aurantia (orange peel mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsHouser, J. / Kozmon, S. / Romano, P.R. / Wimmerova, M.
CitationJournal: PLoS ONE / Year: 2017
Title: Influence of Trp flipping on carbohydrate binding in lectins. An example on Aleuria aurantia lectin AAL.
Authors: Houser, J. / Kozmon, S. / Mishra, D. / Mishra, S.K. / Romano, P.R. / Wimmerova, M. / Koca, J.
History
DepositionJan 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 17, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fucose-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3629
Polymers35,1951
Non-polymers1,1678
Water8,863492
1
A: Fucose-specific lectin
hetero molecules

A: Fucose-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,72418
Polymers70,3902
Non-polymers2,33416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area6450 Å2
ΔGint16 kcal/mol
Surface area24120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.250, 48.630, 57.580
Angle α, β, γ (deg.)90.00, 103.19, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Fucose-specific lectin / Aleuria aurantia lectin / AAL


Mass: 35194.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aleuria aurantia (orange peel mushroom)
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: P18891
#2: Sugar
ChemComp-MFU / methyl alpha-L-fucopyranoside / ALPHA-L-METHYL-FUCOSE / methyl 6-deoxy-alpha-L-galactopyranoside / methyl alpha-L-fucoside / methyl L-fucoside / methyl fucoside


Type: L-saccharide / Mass: 178.183 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C7H14O5
IdentifierTypeProgram
LFucp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-L-fucopyranoseCOMMON NAMEGMML 1.0
o1-methyl-a-L-fucoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 12% PEG6K, 0.12M citrate pH 5.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91801 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91801 Å / Relative weight: 1
ReflectionResolution: 1.14→64.38 Å / Num. obs: 130546 / % possible obs: 99.9 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13
Reflection shellResolution: 1.14→1.17 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 18870 / CC1/2: 0.926 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OFZ

1ofz


Resolution: 1.14→64.38 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.363 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.027 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14646 6572 5 %RANDOM
Rwork0.13806 ---
obs0.13848 123974 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 7.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å2-0.04 Å2
2--0.06 Å20 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.14→64.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 0 78 492 2943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022854
X-RAY DIFFRACTIONr_bond_other_d0.0020.022651
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.943951
X-RAY DIFFRACTIONr_angle_other_deg0.86936162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0725402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13723.814118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.68615443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7551515
X-RAY DIFFRACTIONr_chiral_restr0.0870.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023337
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02706
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5260.6361380
X-RAY DIFFRACTIONr_mcbond_other0.5220.6351379
X-RAY DIFFRACTIONr_mcangle_it0.9110.9561748
X-RAY DIFFRACTIONr_mcangle_other0.9120.9571749
X-RAY DIFFRACTIONr_scbond_it0.5710.6621473
X-RAY DIFFRACTIONr_scbond_other0.5710.6621473
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9150.9712161
X-RAY DIFFRACTIONr_long_range_B_refined5.0056.8013747
X-RAY DIFFRACTIONr_long_range_B_other4.1555.5023364
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.137→1.167 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 534 -
Rwork0.19 8972 -
obs--98.99 %

+
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://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