[English] 日本語
Yorodumi
- PDB-7p1u: Structure of KDNase from Trichophyton Rubrum in complex with 2-ke... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p1u
TitleStructure of KDNase from Trichophyton Rubrum in complex with 2-keto-3-deoxynononic acid
ComponentsExtracellular sialidase/neuraminidase
KeywordsCARBOHYDRATE / Carbohydrate Metabolism / Enzyme Structure / Protein Structure / KDN / KDNase / Sialic Acid / Sialidase
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / metal ion binding / membrane / cytoplasm
Similarity search - Function
BNR repeat-like domain / Sialidase family / Sialidase / Sialidase superfamily
Similarity search - Domain/homology
deamino-alpha-neuraminic acid / exo-alpha-sialidase
Similarity search - Component
Biological speciesTrichophyton rubrum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å
AuthorsGloster, T.M. / McMahon, S.A.
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1516
Polymers84,4302
Non-polymers7214
Water16,069892
1
A: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5753
Polymers42,2151
Non-polymers3602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Extracellular sialidase/neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5753
Polymers42,2151
Non-polymers3602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.450, 74.010, 160.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A4 - 386
2010B4 - 386

-
Components

#1: Protein Extracellular sialidase/neuraminidase


Mass: 42214.945 Da / Num. of mol.: 2
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-KDM / deamino-alpha-neuraminic acid / alpha-deaminoneuraminic acid / 3-deoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid / sialic acid / (2R,4S,5R,6R)-2,4,5-TRIHYDROXY-6-[(1R,2R)-1,2,3-TRIHYDROXYPROPYL]OXANE-2-CARBOXYLIC-ACID


Type: D-saccharide, alpha linking / Mass: 268.218 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C9H16O9
IdentifierTypeProgram
DKdnpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
2-keto-3-deoxy-a-D-nonulopyranosic acidCOMMON NAMEGMML 1.0
a-D-KdnpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
KdnSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 892 / 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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% Peg 3350, 0.2m K formate

-
Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91188 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91188 Å / Relative weight: 1
ReflectionResolution: 0.99→47.73 Å / Num. obs: 405311 / % possible obs: 98.5 % / Redundancy: 5.4 % / CC1/2: 0.999 / Net I/σ(I): 8.9
Reflection shellResolution: 0.99→1.01 Å / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 1 / Num. unique obs: 18293 / CC1/2: 0.7 / % possible all: 89.6

-
Processing

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

2xcy


Resolution: 0.99→47.73 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.158 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 19946 4.9 %RANDOM
Rwork0.218 ---
obs0.2192 385221 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 max: 192.06 Å2 / Biso mean: 12.478 Å2 / Biso min: 5.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2---0.69 Å20 Å2
3---0.42 Å2
Refinement stepCycle: final / Resolution: 0.99→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5857 0 48 900 6805
Biso mean--11.18 27.88 -
Num. residues----766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196297
X-RAY DIFFRACTIONr_bond_other_d0.0060.025626
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.9458585
X-RAY DIFFRACTIONr_angle_other_deg0.852.99413101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1645824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.26323.165278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.097151007
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4411558
X-RAY DIFFRACTIONr_chiral_restr0.1010.2910
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217270
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021332
X-RAY DIFFRACTIONr_rigid_bond_restr5.798311923
X-RAY DIFFRACTIONr_sphericity_free24.2285531
X-RAY DIFFRACTIONr_sphericity_bonded15.034512128
Refine LS restraints NCS

Ens-ID: 1 / Number: 14069 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 0.99→1.016 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.489 1366 -
Rwork0.49 26148 -
all-27514 -
obs--91.16 %

+
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