[English] 日本語
Yorodumi
- PDB-6m77: GH31 alpha-N-acetylgalactosaminidase from Enterococcus faecalis i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6m77
TitleGH31 alpha-N-acetylgalactosaminidase from Enterococcus faecalis in complex with N-acetylgalactosamine
ComponentsLPXTG-motif cell wall anchor domain protein
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / MUCIN / (BETA/ALPHA)8-BARREL / FIBRONECTIN-LIKE
Function / homologyDomain of unknown function (DUF5110) / Glycosyl hydrolases family 31 TIM-barrel domain / 2-acetamido-2-deoxy-beta-D-galactopyranose
Function and homology information
Biological speciesEnterococcus faecalis ATCC 10100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMiyazaki, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K15748 Japan
CitationJournal: Febs Lett. / Year: 2020
Title: Crystal structure of the Enterococcus faecalis alpha-N-acetylgalactosaminidase, a member of the glycoside hydrolase family 31.
Authors: Miyazaki, T. / Park, E.Y.
History
DepositionMar 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Aug 12, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Sep 16, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_entry_details ...entity_src_gen / pdbx_entry_details / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_strain / _pdbx_entry_details.sequence_details / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.4Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LPXTG-motif cell wall anchor domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,2008
Polymers106,6291
Non-polymers5727
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area34940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.596, 83.233, 147.787
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein LPXTG-motif cell wall anchor domain protein


Mass: 106628.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis ATCC 10100 (bacteria)
Strain: ATCC 10100 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE / N-Acetylgalactosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS EOK08638.1 FOR THE PROTEIN.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG3350, 0.2 M ammonium citrate, 5 mM N-acetylgalactosamine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 80809 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.8
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 11575 / CC1/2: 0.844 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M76

6m76


Resolution: 1.9→40.091 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.255 / WRfactor Rwork: 0.21 / SU B: 4.774 / SU ML: 0.134 / Average fsc free: 0.8527 / Average fsc work: 0.8767 / Cross valid method: FREE R-VALUE / ESU R: 0.167 / ESU R Free: 0.157
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2611 4011 4.97 %
Rwork0.217 76695 -
all0.219 --
obs-80706 99.722 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 30.848 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å2-0 Å2-0 Å2
2---0.078 Å20 Å2
3---1.658 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7090 0 36 309 7435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137301
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176451
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.6539901
X-RAY DIFFRACTIONr_angle_other_deg1.3371.58215068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.825907
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92624.734376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.369151180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3881521
X-RAY DIFFRACTIONr_chiral_restr0.0820.2939
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028277
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021483
X-RAY DIFFRACTIONr_nbd_refined0.2010.21429
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.26139
X-RAY DIFFRACTIONr_nbtor_refined0.1710.23477
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.23035
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2405
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0710.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1170.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.170.214
X-RAY DIFFRACTIONr_nbd_other0.2750.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0990.28
X-RAY DIFFRACTIONr_mcbond_it2.8493.2393631
X-RAY DIFFRACTIONr_mcbond_other2.8473.2383630
X-RAY DIFFRACTIONr_mcangle_it3.9244.8374534
X-RAY DIFFRACTIONr_mcangle_other3.9254.8394535
X-RAY DIFFRACTIONr_scbond_it2.8863.4123670
X-RAY DIFFRACTIONr_scbond_other2.8853.4123671
X-RAY DIFFRACTIONr_scangle_it4.1695.0335366
X-RAY DIFFRACTIONr_scangle_other4.1685.0345367
X-RAY DIFFRACTIONr_lrange_it5.62636.3218163
X-RAY DIFFRACTIONr_lrange_other5.60836.2948106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.3313110.3055535X-RAY DIFFRACTION98.9506
1.949-2.0030.3563090.3385387X-RAY DIFFRACTION99.0781
2.003-2.0610.3072650.2965317X-RAY DIFFRACTION99.2532
2.061-2.1240.2952350.2485181X-RAY DIFFRACTION99.4857
2.124-2.1940.272470.2255051X-RAY DIFFRACTION99.9811
2.194-2.2710.2652730.2154817X-RAY DIFFRACTION100
2.271-2.3560.2762700.2074705X-RAY DIFFRACTION99.9598
2.356-2.4520.2932230.2184539X-RAY DIFFRACTION100
2.452-2.5610.2742730.2274302X-RAY DIFFRACTION99.9563
2.561-2.6860.3022070.2274194X-RAY DIFFRACTION99.9319
2.686-2.8310.2671780.2143963X-RAY DIFFRACTION100
2.831-3.0030.2851910.2123774X-RAY DIFFRACTION99.9496
3.003-3.210.261920.2213545X-RAY DIFFRACTION99.9733
3.21-3.4660.2591700.2213309X-RAY DIFFRACTION99.9713
3.466-3.7960.2471340.2083089X-RAY DIFFRACTION99.938
3.796-4.2430.2341600.1872757X-RAY DIFFRACTION100
4.243-4.8970.2441110.1782490X-RAY DIFFRACTION99.7316
4.897-5.9910.2031370.192073X-RAY DIFFRACTION99.8644
5.991-8.4440.191860.1811680X-RAY DIFFRACTION99.9434
8.444-40.0910.184390.169987X-RAY DIFFRACTION98.5591

+
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