[English] 日本語
Yorodumi
- PDB-4c1y: Crystal Structure of Fucose binding lectin from Aspergillus Fumig... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c1y
TitleCrystal Structure of Fucose binding lectin from Aspergillus Fumigatus (AFL) in complex with b-methylfucoside
Components(FUCOSE-SPECIFIC LECTIN ...) x 2
KeywordsSUGAR BINDING PROTEIN / FUCOSIDE
Function / homology
Function and homology information


adhesion of symbiont to host cell surface via host glycoprotein / carbohydrate binding / metal ion binding
Similarity search - Function
Fucose-specific lectin / Fucose-specific lectin / Fungal fucose-specific lectin / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
methyl beta-L-fucopyranoside / DI(HYDROXYETHYL)ETHER / Fucose-specific lectin
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsHouser, J. / Komarek, J. / Kostlanova, N. / Lahmann, M. / Cioci, G. / Varrot, A. / Imberty, A. / Wimmerova, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural Insights Into Aspergillus Fumigatus Lectin Specificity: Afl Binding Sites are Functionally Non-Equivalent.
Authors: Houser, J. / Komarek, J. / Cioci, G. / Varrot, A. / Imberty, A. / Wimmerova, M.
History
DepositionAug 14, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: 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 FLEA
B: FUCOSE-SPECIFIC LECTIN FLEA
C: FUCOSE-SPECIFIC LECTIN FLEA
D: FUCOSE-SPECIFIC LECTIN FLEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,05427
Polymers137,9414
Non-polymers3,11323
Water2,450136
1
A: FUCOSE-SPECIFIC LECTIN FLEA
B: FUCOSE-SPECIFIC LECTIN FLEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,93118
Polymers68,9792
Non-polymers1,95216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-15.4 kcal/mol
Surface area27900 Å2
MethodPQS
2
C: FUCOSE-SPECIFIC LECTIN FLEA
D: FUCOSE-SPECIFIC LECTIN FLEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1249
Polymers68,9632
Non-polymers1,1617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-17.3 kcal/mol
Surface area28200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.211, 90.335, 189.168
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
FUCOSE-SPECIFIC LECTIN ... , 2 types, 4 molecules ABCD

#1: Protein FUCOSE-SPECIFIC LECTIN FLEA


Mass: 34497.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q4WW81
#2: Protein FUCOSE-SPECIFIC LECTIN FLEA


Mass: 34481.270 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q4WW81

-
Sugars , 1 types, 12 molecules

#3: Sugar
ChemComp-MFB / methyl beta-L-fucopyranoside / BETA-L-METHYL-FUCOSE / methyl 6-deoxy-beta-L-galactopyranoside / methyl beta-L-fucoside / methyl L-fucoside / methyl fucoside


Type: L-saccharide / Mass: 178.183 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C7H14O5
IdentifierTypeProgram
LFucp[1Me]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-b-L-fucopyranoseCOMMON NAMEGMML 1.0
o1-methyl-b-L-fucoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 4 types, 147 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.2 Å3/Da / Density % sol: 44.24 % / Description: NONE
Crystal growDetails: 0.2M CACL2, 25% PEG4K, 0.1M TRIS, PH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 21, 2011 / Details: MIRRORS
RadiationMonochromator: SI-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.23→47.29 Å / Num. obs: 56864 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.14
Reflection shellResolution: 2.23→2.29 Å / Rmerge(I) obs: 0.35 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AGI

4agi


Resolution: 2.23→48.14 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.835 / SU B: 9.545 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.432 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.31339 2993 5 %RANDOM
Rwork0.24255 ---
obs0.24611 56864 99.01 %-
Displacement parametersBiso mean: 26.964 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2---1.9 Å20 Å2
3---2.63 Å2
Refinement stepCycle: LAST / Resolution: 2.23→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9754 0 203 136 10093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0210230
X-RAY DIFFRACTIONr_bond_other_d0.0020.029252
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.93713944
X-RAY DIFFRACTIONr_angle_other_deg0.791321205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.30851252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0423.702470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.163151445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2721554
X-RAY DIFFRACTIONr_chiral_restr0.0850.21501
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111758
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022556
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_it1.682.6725020
X-RAY DIFFRACTIONr_mcbond_other1.682.6725019
X-RAY DIFFRACTIONr_mcangle_it2.6824.0026268
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5412.8335210
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.229→2.286 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 215 -
Rwork0.351 4095 -
obs--97.82 %

+
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