[English] 日本語
Yorodumi
- PDB-5fqe: The details of glycolipid glycan hydrolysis by the structural ana... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fqe
TitleThe details of glycolipid glycan hydrolysis by the structural analysis of a family 123 glycoside hydrolase from Clostridium perfringens
ComponentsBETA-N-ACETYLGALACTOSAMINIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / GH123 / GLYCOSPHINGOLIPID / GANGLIOSIDE / GLOBOSIDE / SUBSTRATE- ASSISTED CATALYSIS.
Function / homologyGlycoside hydrolase 123, C-terminal / Glycoside hydrolase 123, N-terminal domain / Glycoside hydrolase 123, catalytic domain / Glycoside hydrolase 123, N-terminal domain / BROMIDE ION / FORMIC ACID / Uncharacterized protein
Function and homology information
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsNoach, I. / Pluvinage, B. / Laurie, C. / Abe, K.T. / Alteen, M. / Vocadlo, D.J. / Boraston, A.B.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: The Details of Glycolipid Glycan Hydrolysis by the Structural Analysis of a Family 123 Glycoside Hydrolase from Clostridium Perfringens
Authors: Noach, I. / Pluvinage, B. / Laurie, C. / Abe, K.T. / Alteen, M. / Vocadlo, D.J. / Boraston, A.B.
History
DepositionDec 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Nov 14, 2018Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_atoms
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-N-ACETYLGALACTOSAMINIDASE
B: BETA-N-ACETYLGALACTOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,398140
Polymers140,4682
Non-polymers10,930138
Water23,0051277
1
A: BETA-N-ACETYLGALACTOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,15976
Polymers70,2341
Non-polymers5,92575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-N-ACETYLGALACTOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,23964
Polymers70,2341
Non-polymers5,00463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.420, 115.030, 135.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein BETA-N-ACETYLGALACTOSAMINIDASE /


Mass: 70234.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A0A0H2YNR7
#2: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical...
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 133 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1277 / 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: 2.48 Å3/Da / Density % sol: 50.46 % / Description: NONE
Crystal growDetails: 0.20 M SODIUM FORMATE, 11% (W/V) POLYETHYLENE GLYCOL 3350, AND 0.1 M HEPES, PH 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97957
DetectorDetector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.5→87.7 Å / Num. obs: 209500 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.2
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.6 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→87.71 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.221 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18515 9845 5 %RANDOM
Rwork0.15813 ---
obs0.15948 188180 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.476 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.53→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9402 0 153 1277 10832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01910043
X-RAY DIFFRACTIONr_bond_other_d0.0020.029048
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.93313702
X-RAY DIFFRACTIONr_angle_other_deg1.017320931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32151246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29325.271516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.751151691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1071537
X-RAY DIFFRACTIONr_chiral_restr0.1120.21436
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211734
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022419
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_it1.3091.4514830
X-RAY DIFFRACTIONr_mcbond_other1.311.4514831
X-RAY DIFFRACTIONr_mcangle_it1.9232.1756094
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1531.6365213
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: 1.53→1.569 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 709 -
Rwork0.212 13924 -
obs--99.3 %

+
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