[English] 日本語
Yorodumi
- PDB-8opz: Crystal structure of a tailspike depolymerase (APK16_gp47) from A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8opz
TitleCrystal structure of a tailspike depolymerase (APK16_gp47) from Acinetobacter phage APK16
ComponentsTailspike depolymerase (APK16_gp47) from Acinetobacter phage APK16
KeywordsVIRAL PROTEIN / bacteriophage / Acinetobacter baumannii / tailspike depolymerase / VIRUS
Biological speciesAcinetobacter phage APK16 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsMatyuta, I.O. / Boyko, K.M. / Nikolaeva, A.Y. / Shneider, M.M. / Timoshina, O.Y. / Miroshnikov, K.A. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1354 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2023
Title: Friunavirus Phage-Encoded Depolymerases Specific to Different Capsular Types of Acinetobacter baumannii .
Authors: Timoshina, O.Y. / Kasimova, A.A. / Shneider, M.M. / Matyuta, I.O. / Nikolaeva, A.Y. / Evseev, P.V. / Arbatsky, N.P. / Shashkov, A.S. / Chizhov, A.O. / Shelenkov, A.A. / Mikhaylova, Y.V. / ...Authors: Timoshina, O.Y. / Kasimova, A.A. / Shneider, M.M. / Matyuta, I.O. / Nikolaeva, A.Y. / Evseev, P.V. / Arbatsky, N.P. / Shashkov, A.S. / Chizhov, A.O. / Shelenkov, A.A. / Mikhaylova, Y.V. / Slukin, P.V. / Volozhantsev, N.V. / Boyko, K.M. / Knirel, Y.A. / Miroshnikov, K.A. / Popova, A.V.
History
DepositionApr 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tailspike depolymerase (APK16_gp47) from Acinetobacter phage APK16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4602
Polymers68,3681
Non-polymers921
Water1,40578
1
A: Tailspike depolymerase (APK16_gp47) from Acinetobacter phage APK16
hetero molecules

A: Tailspike depolymerase (APK16_gp47) from Acinetobacter phage APK16
hetero molecules

A: Tailspike depolymerase (APK16_gp47) from Acinetobacter phage APK16
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 205 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)205,3806
Polymers205,1043
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area31020 Å2
ΔGint-123 kcal/mol
Surface area63410 Å2
Unit cell
Length a, b, c (Å)88.045, 88.045, 254.969
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-960-

HOH

-
Components

#1: Protein Tailspike depolymerase (APK16_gp47) from Acinetobacter phage APK16


Mass: 68368.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter phage APK16 (virus) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris pH 8.5, 2.0M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→84.99 Å / Num. obs: 117005 / % possible obs: 99.8 % / Redundancy: 20.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.25 / Rpim(I) all: 0.057 / Rrim(I) all: 0.256 / Χ2: 0.31 / Net I/σ(I): 4.7 / Num. measured all: 2443418
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 98.5 % / Redundancy: 20.9 % / Rmerge(I) obs: 5.952 / Num. measured all: 120018 / Num. unique obs: 5743 / CC1/2: 0.482 / Rpim(I) all: 1.321 / Rrim(I) all: 6.098 / Χ2: 0.02 / Net I/σ(I) obs: 0.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
DIALSdata reduction
CRANK2phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 1.5→84.99 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.534 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.014 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21471 5830 5 %RANDOM
Rwork0.17473 ---
obs0.17667 111172 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.03 Å2
Baniso -1Baniso -2Baniso -3
1-7.25 Å20 Å20 Å2
2--7.25 Å20 Å2
3----14.5 Å2
Refinement stepCycle: 1 / Resolution: 1.5→84.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4714 0 6 78 4798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0124825
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.0781.6276563
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.935631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.14423.886229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.41615751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4651519
X-RAY DIFFRACTIONr_chiral_restr0.2550.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.023689
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1942.7362527
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.7964.1363157
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.8843.0132296
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.58238.2916772
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.504→1.543 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 408 -
Rwork0.308 8264 -
obs--98.75 %

+
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