[English] 日本語
Yorodumi
- PDB-7p1d: Structure of KDNase from Aspergillus Terrerus in complex with 2-k... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p1d
TitleStructure of KDNase from Aspergillus Terrerus in complex with 2-keto-3-deoxynononic acid
ComponentsSialidase domain-containing protein
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 / deamino-alpha-neuraminic acid / Sialidase domain-containing protein
Function and homology information
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_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

-
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)45,1794
Polymers44,6021
Non-polymers5773
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-12 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.652, 67.045, 93.507
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-743-

HOH

-
Components

#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 BL21(DE3) (bacteria) / References: UniProt: Q0CMX0
#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 / Sialic acid


Type: D-saccharide, alpha linking / Mass: 268.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16O9 / Feature type: SUBJECT OF INVESTIGATION
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-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / 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 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M / 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: 1.69→67.04 Å / Num. obs: 43029 / % possible obs: 98.4 % / Redundancy: 5.2 % / CC1/2: 0.99 / Net I/σ(I): 8.3
Reflection shellResolution: 1.69→1.74 Å / Num. unique obs: 2889 / CC1/2: 0.78

-
Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xcy

2xcy


Resolution: 1.69→67.04 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.378 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 2213 5.1 %RANDOM
Rwork0.2003 ---
obs0.2023 40778 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.28 Å2 / Biso mean: 25.455 Å2 / Biso min: 15.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2---0.71 Å20 Å2
3---0.5 Å2
Refinement stepCycle: final / Resolution: 1.69→67.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2943 0 37 319 3299
Biso mean--29.43 29.8 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023050
X-RAY DIFFRACTIONr_bond_other_d0.0020.022690
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9544142
X-RAY DIFFRACTIONr_angle_other_deg0.8293.0046240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8555381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.68122.95139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83915462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7331528
X-RAY DIFFRACTIONr_chiral_restr0.090.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213449
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02669
LS refinement shellResolution: 1.694→1.738 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 145 -
Rwork0.294 2740 -
all-2885 -
obs--90.44 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.70180.16280.16721.07560.05650.7887-0.05190.11650.0953-0.03460.0679-0.06650.075-0.0063-0.0160.0244-0.0087-0.00290.0155-0.02250.18223.881-20.168-29.053
23.6912-2.3551-2.699912.19587.68015.3647-0.04070.44280.0611-0.9899-0.04620.0366-0.4952-0.08690.08690.2363-0.06190.04730.30070.09560.387320.348-7.995-43.665
36.63662.6718-0.49691.69420.13230.4236-0.19570.37540.7776-0.10590.2090.1384-0.0797-0.0372-0.01330.0621-0.0089-0.03330.04930.01180.35136.071-3.581-31.503
42.3315-0.31730.462.1427-0.16280.9362-0.0386-0.36720.5650.25770.0913-0.2647-0.02610.0686-0.05270.03120.0098-0.02440.0831-0.12920.458213.491-6.936-15.226
52.14280.0174-0.58891.0844-0.09831.77210.0798-0.2932-0.12020.28180.0398-0.35380.13430.2263-0.11960.1060.0124-0.07220.0577-0.03460.343916.1-24.503-13.063
61.93740.1452-0.67020.99070.20344.2283-0.0097-0.1837-0.23360.17120.0499-0.29730.22080.2012-0.04020.07460.0061-0.02390.0327-0.02610.23369.94-27.579-19.407
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 151
2X-RAY DIFFRACTION2A152 - 173
3X-RAY DIFFRACTION3A174 - 206
4X-RAY DIFFRACTION4A207 - 310
5X-RAY DIFFRACTION5A311 - 363
6X-RAY DIFFRACTION6A364 - 403

+
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