[English] 日本語
Yorodumi
- PDB-6tvi: Salmonella typhimurium mutant neuraminidase (D100S)+ DANA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tvi
TitleSalmonella typhimurium mutant neuraminidase (D100S)+ DANA
ComponentsSialidaseNeuraminidase
KeywordsHYDROLASE / Salmonella Typhimurium enzyme / complex / DANA / D100S mutant neuraminidase complexed with DANA / sialidase
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase activity / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / intracellular membrane-bounded organelle / membrane / cytoplasm
Similarity search - Function
Trypanosome sialidase / BNR repeat-like domain / Sialidase family / Sialidase / Sialidase superfamily
Similarity search - Domain/homology
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Sialidase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsGarman, E.F. / Salinger, M.T. / Murray, J.W. / Laver, W.G. / Kuhn, P. / Vimr, E.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: Salmonella typhimurium mutant neuraminidase (D100S)+ DANA
Authors: Garman, E.F. / Salinger, M.T. / Murray, J.W. / Laver, W.G. / Kuhn, P. / Vimr, E.R.
History
DepositionJan 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Category: chem_comp / Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / 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 / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6078
Polymers41,7641
Non-polymers8447
Water8,773487
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint0 kcal/mol
Surface area14160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.068, 81.781, 91.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Sialidase / Neuraminidase / N-acylneuraminate glycohydrolase / Neuraminidase / NANase / STNA


Mass: 41763.547 Da / Num. of mol.: 1 / Mutation: D100S
Source method: isolated from a genetically manipulated source
Details: DANA: 2-deoxy-2,3-dehydro-n-acetyl-neuraminic acid
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Gene: nanH, STM0928 / Plasmid: pSELECT-nanH / Cell line (production host): JM109 / Production host: Escherichia coli (E. coli) / References: UniProt: P29768, exo-alpha-sialidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Sugar ChemComp-DAN / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Neu5Ac2en


Type: D-saccharide / Mass: 291.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO8
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Crystals grown by hanging drop vapour diffusion. A 1:1 mixture of 15mg/ml protein solution and an 8:4 mixture of 3.0M K2HPO4 to 1.4M KH2P04 was placed above a well of an 8:6 solution of 3.0M ...Details: Crystals grown by hanging drop vapour diffusion. A 1:1 mixture of 15mg/ml protein solution and an 8:4 mixture of 3.0M K2HPO4 to 1.4M KH2P04 was placed above a well of an 8:6 solution of 3.0M K2HPO4 to 1.4M KH2PO4. Then serially cryoprotected in situ to 40% glycerol (v/v with mother liquor) in 10% increments over a period of a few minutes.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1→21.96 Å / Num. obs: 188880 / % possible obs: 99.7 % / Redundancy: 5 % / Biso Wilson estimate: 6.4 Å2 / Rrim(I) all: 0.091 / Net I/σ(I): 11.5
Reflection shellResolution: 1→1.02 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 9266 / Rrim(I) all: 0.573 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SIL

3sil


Resolution: 1→21.959 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.129 / WRfactor Rwork: 0.115 / SU B: 0.429 / SU ML: 0.01 / Average fsc free: 0.9796 / Average fsc work: 0.982 / Cross valid method: FREE R-VALUE / ESU R: 0.019 / ESU R Free: 0.02
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1332 5722 3.029 %
Rwork0.1184 183158 -
all0.119 --
obs-188880 99.588 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 8.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.026 Å2-0 Å2-0 Å2
2---0.071 Å20 Å2
3---0.044 Å2
Refinement stepCycle: LAST / Resolution: 1→21.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 56 487 3481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0133416
X-RAY DIFFRACTIONr_bond_other_d0.0030.0183124
X-RAY DIFFRACTIONr_angle_refined_deg2.281.6454654
X-RAY DIFFRACTIONr_angle_other_deg1.6451.5897315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.0685.195461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.85122.767159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1615603
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg2.581152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5121517
X-RAY DIFFRACTIONr_chiral_restr0.1360.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.024172
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02715
X-RAY DIFFRACTIONr_nbd_refined0.2870.2683
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.23085
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21611
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0940.21700
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2384
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.30.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2680.230
X-RAY DIFFRACTIONr_nbd_other0.230.294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2150.251
X-RAY DIFFRACTIONr_mcbond_it1.460.6551712
X-RAY DIFFRACTIONr_mcbond_other1.4590.6541711
X-RAY DIFFRACTIONr_mcangle_it1.6530.9922200
X-RAY DIFFRACTIONr_mcangle_other1.6540.9922201
X-RAY DIFFRACTIONr_scbond_it2.2130.9051704
X-RAY DIFFRACTIONr_scbond_other2.2120.9051705
X-RAY DIFFRACTIONr_scangle_it2.971.2612453
X-RAY DIFFRACTIONr_scangle_other2.971.262454
X-RAY DIFFRACTIONr_lrange_it3.23910.0984027
X-RAY DIFFRACTIONr_lrange_other3.23810.0974028
X-RAY DIFFRACTIONr_rigid_bond_restr8.23936540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.0260.2133920.19813483X-RAY DIFFRACTION99.9208
1.026-1.0540.1784150.16713058X-RAY DIFFRACTION99.8
1.054-1.0850.1524100.13812782X-RAY DIFFRACTION99.758
1.085-1.1180.1063640.112406X-RAY DIFFRACTION99.7968
1.118-1.1550.1023820.07911994X-RAY DIFFRACTION99.5896
1.155-1.1950.0973640.07711526X-RAY DIFFRACTION99.2405
1.195-1.240.0943830.07511248X-RAY DIFFRACTION99.7513
1.24-1.2910.0943570.07710786X-RAY DIFFRACTION100
1.291-1.3480.0983210.08410458X-RAY DIFFRACTION100
1.348-1.4140.0963330.0929927X-RAY DIFFRACTION100
1.414-1.4910.1172950.0999483X-RAY DIFFRACTION99.8672
1.491-1.5810.12940.098949X-RAY DIFFRACTION99.5584
1.581-1.690.1152650.0878439X-RAY DIFFRACTION99.8051
1.69-1.8250.12420.0897903X-RAY DIFFRACTION99.8039
1.825-20.1142310.1087262X-RAY DIFFRACTION99.8667
2-2.2350.1411900.126657X-RAY DIFFRACTION100
2.235-2.5810.191680.1615873X-RAY DIFFRACTION99.8347
2.581-3.1610.1891350.1764997X-RAY DIFFRACTION99.1499
3.161-4.4670.1681200.1443797X-RAY DIFFRACTION97.0275
4.467-21.9590.218610.1882130X-RAY DIFFRACTION92.7997

+
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