[English] 日本語
Yorodumi
- PDB-6mrv: Sialidase26 co-crystallized with DANA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mrv
TitleSialidase26 co-crystallized with DANA
ComponentsSialidase26
KeywordsHYDROLASE / Sialidase / microbiome / Neu5Ac / sialic acid / inflammation / Neu5Ac2en / DANA
Function / homology
Function and homology information


exo-alpha-sialidase activity / ganglioside catabolic process / oligosaccharide catabolic process / intracellular membrane-bounded organelle / membrane / cytoplasm
Similarity search - Function
Sialidase, N-terminal / N-terminal domain of BNR-repeat neuraminidase / Immunoglobulin-like - #1290 / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase ...Sialidase, N-terminal / N-terminal domain of BNR-repeat neuraminidase / Immunoglobulin-like - #1290 / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Sialidase
Similarity search - Component
Biological speciesunidentified bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZaramela, L.S. / Martino, C. / Alisson-Silva, F. / Rees, S.D. / Diaz, S.L. / Chuzel, L. / Ganatra, M.B. / Taron, C.H. / Zuniga, C. / Chang, G. ...Zaramela, L.S. / Martino, C. / Alisson-Silva, F. / Rees, S.D. / Diaz, S.L. / Chuzel, L. / Ganatra, M.B. / Taron, C.H. / Zuniga, C. / Chang, G. / Varki, A. / Zengler, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1444435 United States
Citation
Journal: Nat Microbiol / Year: 2019
Title: Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates.
Authors: Zaramela, L.S. / Martino, C. / Alisson-Silva, F. / Rees, S.D. / Diaz, S.L. / Chuzel, L. / Ganatra, M.B. / Taron, C.H. / Secrest, P. / Zuniga, C. / Huang, J. / Siegel, D. / Chang, G. / Varki, A. / Zengler, K.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
History
DepositionOct 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Apr 22, 2020Group: Data collection / Category: chem_comp / Item: _chem_comp.type
Revision 1.5Jul 29, 2020Group: Derived calculations / Category: struct_site / struct_site_gen / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Oct 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Sialidase26
A: Sialidase26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,9994
Polymers123,4162
Non-polymers5832
Water7,584421
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-11 kcal/mol
Surface area37200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.040, 116.700, 113.636
Angle α, β, γ (deg.)90.000, 106.338, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

-
Components

#1: Protein Sialidase26


Mass: 61708.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified bacterium (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4S2B4D9*PLUS
#2: Sugar ChemComp-DAN / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Neu5Ac2en


Type: D-saccharide / Mass: 291.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17NO8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 6000, 0.1 M Tris-HCl pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99995 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99995 Å / Relative weight: 1
ReflectionResolution: 1.8→60.78 Å / Num. obs: 106390 / % possible obs: 99.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 17.76 Å2 / Net I/σ(I): 6.6
Reflection shellResolution: 1.8→1.83 Å

-
Processing

Software
NameVersionClassification
BOSdata collection
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q6K

4q6k


Resolution: 1.8→60.78 Å / SU ML: 0.2345 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 23.206
RfactorNum. reflection% reflection
Rfree0.2292 9376 4.92 %
Rwork0.2023 --
obs0.2036 106029 90.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.12 Å2
Refinement stepCycle: LAST / Resolution: 1.8→60.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8134 0 40 421 8595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00388360
X-RAY DIFFRACTIONf_angle_d0.780111348
X-RAY DIFFRACTIONf_chiral_restr0.05051279
X-RAY DIFFRACTIONf_plane_restr0.00421455
X-RAY DIFFRACTIONf_dihedral_angle_d11.49914996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.36982940.33875897X-RAY DIFFRACTION88.33
1.82-1.840.34892890.32335892X-RAY DIFFRACTION88.38
1.84-1.860.31953150.30865903X-RAY DIFFRACTION88.8
1.86-1.890.32593230.29115897X-RAY DIFFRACTION88.35
1.89-1.910.27563280.27865889X-RAY DIFFRACTION88.75
1.91-1.940.30863280.28015935X-RAY DIFFRACTION89.06
1.94-1.970.26982850.26935927X-RAY DIFFRACTION89.19
1.97-20.29413190.25155976X-RAY DIFFRACTION89.19
2-2.030.25753210.2465969X-RAY DIFFRACTION89.69
2.03-2.060.26332810.24586008X-RAY DIFFRACTION89.61
2.06-2.10.27573370.24955934X-RAY DIFFRACTION89.75
2.1-2.130.28422970.23476009X-RAY DIFFRACTION90.19
2.13-2.180.2713380.23085967X-RAY DIFFRACTION90.08
2.18-2.220.2543150.2195993X-RAY DIFFRACTION89.91
2.22-2.270.24512870.20856025X-RAY DIFFRACTION90.38
2.27-2.320.21693000.20516097X-RAY DIFFRACTION90.31
2.32-2.380.22713330.20286019X-RAY DIFFRACTION90.61
2.38-2.440.23893110.20596060X-RAY DIFFRACTION90.88
2.44-2.510.2163200.19856054X-RAY DIFFRACTION90.8
2.51-2.60.22572770.20016151X-RAY DIFFRACTION91.38
2.6-2.690.22653020.20546026X-RAY DIFFRACTION91.35
2.69-2.80.25013240.19636131X-RAY DIFFRACTION91.6
2.8-2.920.2172530.19946177X-RAY DIFFRACTION91.83
2.92-3.080.24963180.20056114X-RAY DIFFRACTION91.81
3.08-3.270.21873110.20756179X-RAY DIFFRACTION92.16
3.27-3.520.20253340.19786048X-RAY DIFFRACTION91.43
3.52-3.880.21693210.17886096X-RAY DIFFRACTION91.03
3.88-4.440.17523270.14786107X-RAY DIFFRACTION92.24
4.44-5.590.16253400.12796420X-RAY DIFFRACTION96.23
5.59-60.810.17473480.15256445X-RAY DIFFRACTION96.86

+
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