[English] 日本語
Yorodumi
- PDB-4j27: Crystal structure of a gh29 alpha-l-fucosidase gh29 from bacteroi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j27
TitleCrystal structure of a gh29 alpha-l-fucosidase gh29 from bacteroides thetaiotaomicron in a novel crystal form
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE / Alpha-L-fucosidase
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 / Alpha-L-fucosidase / Glycoside hydrolase, family 29 / 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 / Alpha-L-fucosidase / Glycoside hydrolase, family 29 / 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
IMIDAZOLE / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 Å
AuthorsWright, D.W.
CitationJournal: Bioorg.Med.Chem. / Year: 2013
Title: Three dimensional structure of a bacterial alpha-l-fucosidase with a 5-membered iminocyclitol inhibitor.
Authors: Wright, D.W. / Moreno-Vargas, A.J. / Carmona, A.T. / Robina, I. / Davies, G.J.
History
DepositionFeb 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 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)105,26015
Polymers104,1622
Non-polymers1,09813
Water19,0781059
1
A: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5957
Polymers52,0811
Non-polymers5146
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6648
Polymers52,0811
Non-polymers5847
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.150, 96.550, 97.270
Angle α, β, γ (deg.)90.000, 91.300, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 35 - 471 / Label seq-ID: 1 - 437

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

-
Components

#1: Protein Alpha-L-fucosidase


Mass: 52080.930 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 35-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8A3I4
#2: Chemical
ChemComp-IMD / IMIDAZOLE


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


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


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


Mass: 18.015 Da / Num. of mol.: 1059 / 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: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 17% PEG 6K, 0.124M ammonium sulfate, 0.1M imidazole 2 parts protein: 3 mother liquor, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 21, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.59→30.666 Å / Num. all: 164706 / Num. obs: 164706 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.112 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.59-1.683.70.8780.988387239670.87899.9
1.68-1.783.80.5831.385810227210.583100
1.78-1.93.80.3692.180897213360.369100
1.9-2.053.80.2213.475563198670.221100
2.05-2.253.80.1475.169763183020.147100
2.25-2.523.80.17.463417165760.1100
2.52-2.93.80.0749.556011146080.074100
2.9-3.563.80.0669.247642124090.066100
3.56-5.033.80.053113679695930.053100
5.03-30.6663.80.03417.42003853270.03499.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WVV

2wvv


Resolution: 1.59→30.666 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.1694 / WRfactor Rwork: 0.1497 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8693 / SU B: 1.577 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0654 / SU Rfree: 0.0655 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1775 8454 5 %RANDOM
Rwork0.1577 ---
obs0.1587 159881 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.97 Å2 / Biso mean: 15.8145 Å2 / Biso min: 5.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å2-0.29 Å2
2--0.03 Å20 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.59→30.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7075 0 69 1059 8203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.027468
X-RAY DIFFRACTIONr_bond_other_d0.0050.026815
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.93710159
X-RAY DIFFRACTIONr_angle_other_deg1.056315719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8055915
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03624.157356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.888151224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7641536
X-RAY DIFFRACTIONr_chiral_restr0.0970.21035
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218480
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021798
X-RAY DIFFRACTIONr_mcbond_it1.1011.3123549
X-RAY DIFFRACTIONr_mcbond_other1.11.3113548
X-RAY DIFFRACTIONr_mcangle_it1.7191.9624444
Refine LS restraints NCS

Ens-ID: 1 / Number: 26913 / 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: 1.591→1.632 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 662 -
Rwork0.288 11719 -
all-12381 -
obs--99.93 %

+
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