[English] 日本語
Yorodumi
- PDB-1hl9: CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA ALPHA-FUCOSIDASE IN COMP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hl9
TitleCRYSTAL STRUCTURE OF THERMOTOGA MARITIMA ALPHA-FUCOSIDASE IN COMPLEX WITH A MECHANISM BASED INHIBITOR
ComponentsPUTATIVE ALPHA-L-FUCOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / ALPHA-L-FUCOSIDASE / GLYCOSYL-ENZYME INTERMEDIATE / THERMOSTABLE
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
2-deoxy-2-fluoro-beta-L-fucopyranose / Alpha-L-fucosidase, putative
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSulzenbacher, G. / Bignon, C. / Bourne, Y. / Henrissat, B.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of Thermotoga Maritima {Alpha}-L-Fucosidase: Insights Into the Catalytic Mechanism and the Molecular Basis for Fucosidosis
Authors: Sulzenbacher, G. / Bignon, C. / Nishimura, T. / Tarling, C.A. / Withers, S.G. / Henrissat, B. / Bourne, Y.
History
DepositionMar 14, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 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 / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 13, 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PUTATIVE ALPHA-L-FUCOSIDASE
B: PUTATIVE ALPHA-L-FUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9624
Polymers104,6302
Non-polymers3322
Water3,765209
1
A: PUTATIVE ALPHA-L-FUCOSIDASE
B: PUTATIVE ALPHA-L-FUCOSIDASE
hetero molecules

A: PUTATIVE ALPHA-L-FUCOSIDASE
B: PUTATIVE ALPHA-L-FUCOSIDASE
hetero molecules

A: PUTATIVE ALPHA-L-FUCOSIDASE
B: PUTATIVE ALPHA-L-FUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,88712
Polymers313,8906
Non-polymers9976
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
Unit cell
Length a, b, c (Å)172.157, 172.157, 167.331
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2026-

HOH

21B-2020-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.67846, -0.73296, -0.04956), (-0.73266, 0.68004, -0.02741), (0.05379, 0.01771, -0.9984)
Vector: 2.70326, 1.89408, 83.7312)

-
Components

#1: Protein PUTATIVE ALPHA-L-FUCOSIDASE


Mass: 52315.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ORF TM0306 / Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9WYE2, alpha-L-fucosidase
#2: Sugar ChemComp-FUF / 2-deoxy-2-fluoro-beta-L-fucopyranose / 2,6-DIDEOXY-2-FLUORO-BETA-L-LYXO-HEXOPYRANOSE / 2,6-dideoxy-2-fluoro-beta-L-galactopyranose / 2-deoxy-2-fluoro-beta-L-fucose / 2-deoxy-2-fluoro-L-fucose / 2-deoxy-2-fluoro-fucose


Type: L-saccharide, beta linking / Mass: 166.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11FO4
IdentifierTypeProgram
b-L-Fucp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Compound detailsALPHA-L-FUCOSIDASE BELONGS TO GLYCOSYL HYDROLASASE FAMILY 29. THE ENZYME PERFORMS CATALYSIS WITH ...ALPHA-L-FUCOSIDASE BELONGS TO GLYCOSYL HYDROLASASE FAMILY 29. THE ENZYME PERFORMS CATALYSIS WITH RETENTION OF CONFIGURATION AT THE ANOMERIC CARBON. THE COORDINATES GIVEN DEFINE THE STRUCTURE OF ALPHA-L-FUCOSIDASE IN COMPLEX WITH 2-DEOXY-2-FLUORO-FUCOSE. TWO SPECIES ARE PRESENT IN THE CRYSTAL, ONE IS THE 2-DEOXY-2-FLUORO-FUCOSYL-ENZYME INTERMEDIATE, WITH 2-DEOXY-2-FLUORO-FUCOSE COVALENTLY BOUND TO THE NUCLEOPHILE ASP 224,THE OTHER SPECIES IS THE REACTION PRODUCT 2-DEOXY-2-FLUORO-FUCOSE BOUND TO THE ACTIVE SITE. THE LATTER HAS UNDERGONE MUTAROTATION AND IS PRESENT AS THE BETA-CONFORMER. THE TWO SPECIES ARE OVERLAPPING AND HAVE BEEN REFINED WITH PARTIAL OCCUPANCY.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47 %
Crystal growpH: 8
Details: 18% PEG600, 5% JEFFAMINE M600, 100 MM TRIS-HCL PH 8.0, PROTEIN CONCENTRATION 5 MG/ML THE INHIBITOR WAS INTRODUCED BY SHORT SOAKING OF A NATIVE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 11, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.25→55.9 Å / Num. obs: 37238 / % possible obs: 89.4 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.1
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 4 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 1.8 / % possible all: 89.4

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HL8

1hl8


Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.362 / SU ML: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.411 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TWO OVERLAPPING SPECIES ARE PRESENT IN THE ACTIVE SITE AND HAVE BEEN REFINED WITH PARTIAL OCCUPANCIES.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2918 7.3 %RANDOM
Rwork0.181 ---
obs0.184 37138 90.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.23 Å20 Å2
2--0.47 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7029 0 22 209 7260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0217358
X-RAY DIFFRACTIONr_bond_other_d0.0020.026359
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.9419919
X-RAY DIFFRACTIONr_angle_other_deg0.796314813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0375842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.21014
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028029
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021623
X-RAY DIFFRACTIONr_nbd_refined0.1850.21454
X-RAY DIFFRACTIONr_nbd_other0.230.27196
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.24073
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2264
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.251
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.2150
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.79224205
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4033.56779
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.15833148
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.84843139
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: 2.25→2.31 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 239
Rwork0.209 2673
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0588-0.30450.18450.9078-0.06491.1590.0591-0.35130.18550.048-0.0056-0.0037-0.1724-0.1165-0.05360.0259-0.0180.02630.0861-0.03190.0344-22.63714.82661.838
24.0771-0.6611-0.35281.3053-0.96152.60210.04230.1090.0062-0.1586-0.02120.1661-0.0336-0.1464-0.02110.11410.0996-0.05930.1062-0.01390.1373-50.51124.85240.125
30.9552-0.13270.01063.4082-0.09071.23380.01930.0680.1451-0.30870.07430.3779-0.2284-0.1453-0.09360.090.0139-0.02850.05720.06160.10833.90527.05421.185
42.63211.8863-0.0926.4192-0.54653.55140.0548-0.22040.21050.94020.063-0.2278-0.4360.3073-0.11780.5090.0345-0.05350.1432-0.11340.320117.09554.93241.189
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 360
2X-RAY DIFFRACTION2A361 - 448
3X-RAY DIFFRACTION3B7 - 360
4X-RAY DIFFRACTION4B361 - 448

+
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://pdbjlvh1.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