[English] 日本語
Yorodumi
- PDB-4jfs: Crystal structure of a bacterial fucosidase with iminosugar inhib... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jfs
TitleCrystal structure of a bacterial fucosidase with iminosugar inhibitor 4-epi-(+)-Codonopsinine
Componentsalpha-L-fucosidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / alpha-L-fucosidase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome
Similarity search - Function
Alpha-L-fucosidase, metazoa-type / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...Alpha-L-fucosidase, metazoa-type / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-16Z / IMIDAZOLE / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWright, D.W. / Davies, G.J.
CitationJournal: Chemistry / Year: 2013
Title: alpha-L-fucosidase inhibition by pyrrolidine-ferrocene hybrids: rationalization of ligand-binding properties by structural studies.
Authors: Hottin, A. / Wright, D.W. / Steenackers, A. / Delannoy, P. / Dubar, F. / Biot, C. / Davies, G.J. / Behr, J.B.
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: alpha-L-fucosidase
B: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,69715
Polymers104,1622
Non-polymers1,53513
Water15,349852
1
A: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7147
Polymers52,0811
Non-polymers6336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9838
Polymers52,0811
Non-polymers9027
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.430, 95.770, 97.111
Angle α, β, γ (deg.)90.000, 90.810, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 35 - 470 / Label seq-ID: 1 - 436

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein alpha-L-fucosidase /


Mass: 52080.930 Da / Num. of mol.: 2 / Fragment: RESIDUES 35-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Plasmid: pET-YSBLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8A3I4

-
Non-polymers , 6 types, 865 molecules

#2: Chemical ChemComp-16Z / (2S,3S,4R,5S)-2-(4-methoxyphenyl)-1,5-dimethylpyrrolidine-3,4-diol / 4-epi-(+)-Codonopsinine


Mass: 237.295 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19NO3
#3: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 852 / 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: 3.05 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.13 M ammonium sulfate, 12% PEG 6K, 0.1M imidazole pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: PILATUS 2M / Detector: PIXEL / Date: Mar 8, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.578→97.101 Å / Num. all: 83920 / Num. obs: 83920 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.099 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.113.90.451.747345122310.4599.6
2.11-2.243.90.3232.445425116310.32399.6
2.24-2.393.90.2273.342582108730.22799.5
2.39-2.583.90.1744.339631101240.17499.4
2.58-2.833.90.1216.13627993540.12199.4
2.83-3.163.90.0878.23258484320.08799.3
3.16-3.653.80.0689.42833074940.06899.7
3.65-4.473.70.0599.92316662790.05998.9
4.47-6.323.70.05111.41737647500.05196.1
6.32-36.2733.90.0319.31081027520.0399.3

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J27

4j27


Resolution: 2→97.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.1503 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8785 / SU B: 3.416 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1316 / SU Rfree: 0.1246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. THE COORDINATES FROM 4J27 WERE CONVERTED INTO THE (ALMOST) ISOMORPHOUS CELL OF 4JFS TO BUILD A STARTING ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. THE COORDINATES FROM 4J27 WERE CONVERTED INTO THE (ALMOST) ISOMORPHOUS CELL OF 4JFS TO BUILD A STARTING MODEL DIRECTLY. THE RFREE FLAG FROM 4J27 WAS USED FOR THIS DATASET.
RfactorNum. reflection% reflectionSelection details
Rfree0.1921 4187 5 %AS 4J27
Rwork0.1566 ---
obs0.1584 83899 99.11 %-
all-83920 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86 Å2 / Biso mean: 25.8593 Å2 / Biso min: 13.11 Å2
Baniso -1Baniso -2Baniso -3
1-2.6 Å20 Å2-0.82 Å2
2---0.01 Å20 Å2
3----2.58 Å2
Refinement stepCycle: LAST / Resolution: 2→97.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7031 0 100 852 7983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.027427
X-RAY DIFFRACTIONr_bond_other_d0.0060.026711
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.9410115
X-RAY DIFFRACTIONr_angle_other_deg1.0733.00215455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9645901
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54224.254355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.539151181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9931534
X-RAY DIFFRACTIONr_chiral_restr0.10.21033
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218449
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021799
X-RAY DIFFRACTIONr_mcbond_it1.8522.363529
X-RAY DIFFRACTIONr_mcbond_other1.852.3593528
X-RAY DIFFRACTIONr_mcangle_it2.5633.5274416
Refine LS restraints NCS

Ens-ID: 1 / Number: 26798 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 308 -
Rwork0.231 5841 -
all-6149 -
obs--99.43 %

+
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