[English] 日本語
Yorodumi
- PDB-7p1e: Structure of KDNase from Aspergillus Terrerus in complex with 2,3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p1e
TitleStructure of KDNase from Aspergillus Terrerus in complex with 2,3-difluoro-2-keto-3-deoxynononic acid
ComponentsSialidase domain-containing protein
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 / intracellular membrane-bounded organelle / metal ion binding / membrane / cytoplasm
Similarity search - Function
BNR repeat-like domain / Sialidase family / Sialidase / Sialidase superfamily
Similarity search - Domain/homology
Chem-FKD / Chem-K99 / exo-alpha-sialidase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 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 1, 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sialidase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4367
Polymers44,6021
Non-polymers8346
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-23 kcal/mol
Surface area14210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.348, 66.743, 92.635
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-604-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Sialidase domain-containing protein


Mass: 44602.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (strain NIH 2624 / FGSC A1156) (mold)
Strain: NIH 2624 / FGSC A1156 / Gene: ATEG_04964 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0CMX0

-
Sugars , 2 types, 2 molecules

#2: Sugar ChemComp-FKD / 3-deoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid / 3-deoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulosonic acid / 3-deoxy-3-fluoro-D-erythro-L-manno-non-2-ulosonic acid / 3-deoxy-3-fluoro-D-erythro-manno-non-2-ulosonic acid


Type: L-saccharide, alpha linking / Mass: 286.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15FO9 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-K99 / (2R,3R,4R,5R,6S)-2,3-bis(fluoranyl)-4,5-bis(oxidanyl)-6-[(1R,2R)-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid / (2R,3R,4R,5R,6S)-2,3-DIFLUORO-4,5-DIHYDROXY-6-[(1R,2R)-1,2,3-TRIHYDROXYPROPYL]OXANE-2-CARBOXYLIC ACID


Type: D-saccharide / Mass: 288.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14F2O8 / Feature type: SUBJECT OF INVESTIGATION

-
Non-polymers , 4 types, 357 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 20% PEG 6K, 0.1M MES pH6 , 0.2M Calcium Chloride

-
Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 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: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.53→61.35 Å / Num. obs: 58094 / % possible obs: 99.8 % / Redundancy: 2.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.109 / Net I/σ(I): 7.3
Reflection shellResolution: 1.53→1.57 Å / Redundancy: 2.6 % / Rmerge(I) obs: 1.272 / Mean I/σ(I) obs: 1 / Num. unique obs: 4263 / CC1/2: 0.53 / % possible all: 99.9

-
Processing

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

2xcy


Resolution: 1.53→61.35 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.09 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 2893 5 %RANDOM
Rwork0.1857 ---
obs0.1873 55146 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.89 Å2 / Biso mean: 19.55 Å2 / Biso min: 10.6 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2--0.06 Å20 Å2
3---0.95 Å2
Refinement stepCycle: final / Resolution: 1.53→61.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 51 353 3345
Biso mean--23.08 27.88 -
Num. residues----383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023066
X-RAY DIFFRACTIONr_bond_other_d0.0010.022706
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.964161
X-RAY DIFFRACTIONr_angle_other_deg0.7453.0036276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6875382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91322.878139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.20115462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5511528
X-RAY DIFFRACTIONr_chiral_restr0.0780.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213453
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02673
LS refinement shellResolution: 1.53→1.566 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.29 174 -
Rwork0.3 3761 -
obs--92.15 %

+
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