[English] 日本語
Yorodumi
- PDB-7p1s: Structure of KDNase from Trichophyton Rubrum in complex with 2,3-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p1s
TitleStructure of KDNase from Trichophyton Rubrum in complex with 2,3-didehydro-2,3-dideoxy-D-glycero-D-galacto-nonulosonic acid.
ComponentsExtracellular sialidase/neuraminidase
KeywordsCARBOHYDRATE / Carbohydrate Metabolism / Enzyme Structure / Protein Structure / KDN / KDNase / Sialic Acid / Sialidase
Function / homologyBNR repeat-like domain / exo-alpha-sialidase activity / Sialidase family / Sialidase / Sialidase superfamily / metal ion binding / Chem-KFN / Extracellular sialidase/neuraminidase
Function and homology information
Biological speciesTrichophyton rubrum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsGloster, T.M. / McMahon, S.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Kinetic and Structural Characterization of Sialidases (Kdnases) from Ascomycete Fungal Pathogens.
Authors: Nejatie, A. / Steves, E. / Gauthier, N. / Baker, J. / Nesbitt, J. / McMahon, S.A. / Oehler, V. / Thornton, N.J. / Noyovitz, B. / Khazaei, K. / Byers, B.W. / Zandberg, W.F. / Gloster, T.M. / ...Authors: Nejatie, A. / Steves, E. / Gauthier, N. / Baker, J. / Nesbitt, J. / McMahon, S.A. / Oehler, V. / Thornton, N.J. / Noyovitz, B. / Khazaei, K. / Byers, B.W. / Zandberg, W.F. / Gloster, T.M. / Moore, M.M. / Bennet, A.J.
History
DepositionJul 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Extracellular sialidase/neuraminidase
B: Extracellular sialidase/neuraminidase
C: Extracellular sialidase/neuraminidase
D: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,95312
Polymers168,8604
Non-polymers1,0938
Water13,799766
1
A: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4883
Polymers42,2151
Non-polymers2732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4883
Polymers42,2151
Non-polymers2732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4883
Polymers42,2151
Non-polymers2732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4883
Polymers42,2151
Non-polymers2732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.646, 179.008, 97.292
Angle α, β, γ (deg.)90.000, 104.040, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A5 - 383
2010B5 - 383
1020A5 - 383
2020C5 - 383
1030A5 - 383
2030D5 - 383
1040B4 - 384
2040C4 - 384
1050B4 - 384
2050D4 - 384
1060C4 - 384
2060D4 - 384

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Extracellular sialidase/neuraminidase


Mass: 42214.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichophyton rubrum (fungus) / Gene: A7C99_5399 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A178EUH2
#2: Sugar
ChemComp-KFN / 2,6-anhydro-3-deoxy-D-glycero-D-galacto-non-2-enonic acid / (4S,5R,6R)-4,5-DIHYDROXY-6-[(1R,2R)-1,2,3-TRIHYDROXYPROPYL]-5,6-DIHYDRO-4H-PYRAN-2-CARBOXYLIC ACID


Type: D-saccharide / Mass: 250.203 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 25% PEG 1500 0.1M SPG pH 8

-
Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.92→179.01 Å / Num. obs: 113657 / % possible obs: 92.5 % / Redundancy: 2.9 % / CC1/2: 0.97 / Rmerge(I) obs: 0.145 / Net I/σ(I): 4.6
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4982 / CC1/2: 0.49 / % possible all: 55.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XCY

2xcy


Resolution: 1.92→179.01 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.897 / SU B: 7.704 / SU ML: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2888 5690 5 %RANDOM
Rwork0.2598 ---
obs0.2612 107924 92.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.97 Å2 / Biso mean: 31.141 Å2 / Biso min: 9.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20.46 Å2
2--0.97 Å20 Å2
3----1.21 Å2
Refinement stepCycle: final / Resolution: 1.92→179.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11688 0 72 766 12526
Biso mean--24.59 29.47 -
Num. residues----1523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01912035
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210790
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.94916318
X-RAY DIFFRACTIONr_angle_other_deg0.747325077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9351519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.93523.26546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.808151916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.52115108
X-RAY DIFFRACTIONr_chiral_restr0.0740.21723
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022528
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A128570.05
12B128570.05
21A128350.05
22C128350.05
31A128050.05
32D128050.05
41B129730.05
42C129730.05
51B129170.05
52D129170.05
61C129540.04
62D129540.04
LS refinement shellResolution: 1.92→1.968 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.377 251 -
Rwork0.36 4729 -
obs--54.99 %

+
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