[English] 日本語
Yorodumi
- PDB-7esq: Structure and mutation analysis of the hexameric P4 from Pseudomo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7esq
TitleStructure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage phiYY
ComponentsPackaging NTPase
KeywordsHYDROLASE / Cystoviruses / phiYY P4 / NTPase / VIRAL PROTEIN
Function / homologyPackaging enzyme P4 / ATPase P4 of dsRNA bacteriophage phi-12 / viral genome packaging / P-loop containing nucleoside triphosphate hydrolase / metal ion binding / DI(HYDROXYETHYL)ETHER / PYROPHOSPHATE / Packaging NTPase
Function and homology information
Biological speciesPseudomonas phage phiYY (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsZhang, C.Y. / Jin, T.C.
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Structure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage phiYY.
Authors: Zhang, C. / Li, Y. / Samad, A. / Zheng, P. / Ji, Z. / Chen, F. / Zhang, H. / Jin, T.
History
DepositionMay 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Packaging NTPase
B: Packaging NTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,50610
Polymers74,6772
Non-polymers8298
Water4,576254
1
A: Packaging NTPase
B: Packaging NTPase
hetero molecules

A: Packaging NTPase
B: Packaging NTPase
hetero molecules

A: Packaging NTPase
B: Packaging NTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,51830
Polymers224,0316
Non-polymers2,48724
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area24500 Å2
ΔGint-182 kcal/mol
Surface area56410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.260, 170.260, 170.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

-
Components

#1: Protein Packaging NTPase


Mass: 37338.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage phiYY (bacteriophage)
Gene: phiYY_sL4 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1U9AK63
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 200 mM NH4 tartrate, 20% PEG2000 MME, phosphate pH 7.9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→40.13 Å / Num. obs: 687024 / % possible obs: 99.8 % / Redundancy: 9.8 % / CC1/2: 1 / Net I/σ(I): 26.68
Reflection shellResolution: 1.85→1.96 Å / Num. unique obs: 112408 / CC1/2: 0.718

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4blp

4blp


Resolution: 1.85→40.13 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2041 3479 4.99 %
Rwork0.1855 66252 -
obs0.1864 69731 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.12 Å2 / Biso mean: 45.7793 Å2 / Biso min: 29.13 Å2
Refinement stepCycle: final / Resolution: 1.85→40.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3899 0 48 254 4201
Biso mean--51.47 49.61 -
Num. residues----528
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.870.3761300.3222473260394
1.87-1.90.28171380.270626352773100
1.9-1.930.33581400.276626632803100
1.93-1.960.25141400.239626332773100
1.96-1.990.26971380.226526432781100
1.99-2.020.23331390.213826362775100
2.03-2.060.24231420.215526382780100
2.06-2.10.2491360.212526362772100
2.1-2.140.20151360.197926242760100
2.14-2.190.20991420.1926522794100
2.19-2.240.24751410.204326682809100
2.24-2.30.2221380.200726072745100
2.3-2.360.22971420.198426512793100
2.36-2.430.24141400.204926792819100
2.43-2.510.20671390.20426272766100
2.51-2.60.22281380.204526392777100
2.6-2.70.21341370.202526682805100
2.7-2.820.22871370.206126492786100
2.83-2.970.23731390.202126742813100
2.97-3.160.23881360.193526502786100
3.16-3.40.19251420.191326912833100
3.41-3.750.1771390.176426662805100
3.75-4.290.17621370.159926692806100
4.29-5.390.19021460.158626972843100
5.4-40.130.17661470.171927842931100

+
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