[English] 日本語
Yorodumi
- PDB-1hl8: CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA ALPHA-FUCOSIDASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hl8
TitleCRYSTAL STRUCTURE OF THERMOTOGA MARITIMA ALPHA-FUCOSIDASE
ComponentsPUTATIVE ALPHA-L-FUCOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / ALPHA-L-FUCOSIDASE / 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
Alpha-L-fucosidase, putative
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 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 1.0Jan 15, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)104,6302
Polymers104,6302
Non-polymers00
Water2,918162
1
A: PUTATIVE ALPHA-L-FUCOSIDASE
B: PUTATIVE ALPHA-L-FUCOSIDASE

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

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


Theoretical massNumber of molelcules
Total (without water)313,8906
Polymers313,8906
Non-polymers00
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)172.462, 172.462, 167.414
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
11B-2016-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.68906, -0.72382, -0.03587), (-0.72345, 0.68993, -0.02484), (0.04273, 0.00883, -0.99905)
Vector: 2.16501, 1.65996, 83.38777)

-
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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.
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 47.6 %
Description: THE STRUCTURE WAS SOLVED BY MAD, BUT REFINED AGAINST NATIVE DATA ONLY
Crystal growpH: 8
Details: 18 % PEG600, 5 % JEFFAMINE, M-600 100 MM TRIS-HCL PH 8.0, PROTEIN CONC. 5 MG/ML
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15.0 mg/mlprotein1drop
218 %(w/v)PEG60001reservoir
3100 mMTris-HCl1reservoirpH8.0
45 %Jeffamine M-6001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 3, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→37.3 Å / Num. obs: 36833 / % possible obs: 99.1 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.9
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 1.8 / % possible all: 99.1
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 37 Å / % possible obs: 99.3 % / Redundancy: 5.7 % / Num. measured all: 212598 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 99.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 1.8

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→37.27 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.298 / SU ML: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.525 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS RESIDUES SER 14 A, ARG 16 A, LYS 138 A, ARG 378 A, SER 14 B AND ARG 16 A ARE PRESENT IN DOUBLE DOUBLE CONFORMATION
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2642 7.1 %RANDOM
Rwork0.185 ---
obs0.188 34433 99.1 %-
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 parameters
Baniso -1Baniso -2Baniso -3
1-1.23 Å20.62 Å20 Å2
2--1.23 Å20 Å2
3----1.85 Å2
Refinement stepCycle: LAST / Resolution: 2.4→37.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7037 0 0 162 7199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0217303
X-RAY DIFFRACTIONr_bond_other_d0.0020.026377
X-RAY DIFFRACTIONr_angle_refined_deg1.1031.9369915
X-RAY DIFFRACTIONr_angle_other_deg0.782314847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9435842
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_restr0.0690.21003
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028050
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021643
X-RAY DIFFRACTIONr_nbd_refined0.180.21402
X-RAY DIFFRACTIONr_nbd_other0.2130.27171
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.24168
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2180
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0920.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.2171
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3611.54212
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.68926798
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.96633091
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6214.53114
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: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 197
Rwork0.222 2487
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)
12.0213-0.27710.11580.9561-0.20771.9720.0055-0.27690.24890.15060.14140.0944-0.523-0.456-0.14690.15220.14060.08030.2050.01280.0945-22.578215.445661.6505
24.5278-0.5245-0.4267-0.1212-1.40884.6012-0.052-0.17190.0755-0.08150.13850.284-0.3494-0.4159-0.08650.24650.2952-0.02950.40650.07050.3168-50.358525.44439.9618
31.01590.1710.26421.64560.51732.15530.00260.08140.2235-0.22820.03240.0464-0.75220.0896-0.0350.3023-0.04940.02510.03710.03640.11374.41826.885120.9995
42.79661.6406-0.87055.3735-1.32671.6330.2811-0.70671.04980.5825-0.11080.0187-0.40370.2394-0.17020.7845-0.27810.13380.3226-0.30970.602617.159554.920341.3475
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 360
2X-RAY DIFFRACTION2A361 - 447
3X-RAY DIFFRACTION3B7 - 360
4X-RAY DIFFRACTION4B361 - 447
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 37 Å / Rfactor Rfree: 0.2284 / Rfactor Rwork: 0.1852
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.008
X-RAY DIFFRACTIONr_angle_d1.1

+
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