[English] 日本語
Yorodumi
- PDB-4yeg: Characterisation of Polyphosphate Kinase 2 from the Intracellular... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yeg
TitleCharacterisation of Polyphosphate Kinase 2 from the Intracellular Pathogen Francisella tularensis
ComponentsPolyphosphate kinase 2
KeywordsTRANSFERASE / polyphosphate kinase enzyme
Function / homology
Function and homology information


phosphorus metabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / polyphosphate kinase activity / metal ion binding
Similarity search - Function
Polyphosphate kinase 2, PA0141 / Polyphosphate phosphotransferase / Polyphosphate kinase-2-related / Polyphosphate kinase 2 (PPK2) / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / ADP/GDP-polyphosphate phosphotransferase
Similarity search - Component
Biological speciesFrancisella tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsParnell, A.E. / Roach, P.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
DTRAHDTRA-11-1-007 United Kingdom
CitationJournal: Biosci.Rep. / Year: 2016
Title: Biochemical and structural characterization of polyphosphate kinase 2 from the intracellular pathogen Francisella tularensis.
Authors: Batten, L.E. / Parnell, A.E. / Wells, N.J. / Murch, A.L. / Oyston, P.C. / Roach, P.L.
History
DepositionFeb 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Jun 1, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyphosphate kinase 2
B: Polyphosphate kinase 2
C: Polyphosphate kinase 2
D: Polyphosphate kinase 2


Theoretical massNumber of molelcules
Total (without water)131,8564
Polymers131,8564
Non-polymers00
Water6,900383
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-21 kcal/mol
Surface area48790 Å2
2
A: Polyphosphate kinase 2
D: Polyphosphate kinase 2


Theoretical massNumber of molelcules
Total (without water)65,9282
Polymers65,9282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-9 kcal/mol
Surface area25600 Å2
MethodPISA
3
B: Polyphosphate kinase 2
C: Polyphosphate kinase 2


Theoretical massNumber of molelcules
Total (without water)65,9282
Polymers65,9282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-9 kcal/mol
Surface area24130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.790, 88.890, 163.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Polyphosphate kinase 2


Mass: 32963.930 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis (bacteria)
Gene: ppk2, DR80_1140, DR81_590, DR84_1109, DR85_1285, DR86_904, DR87_59
Production host: Escherichia coli (E. coli)
References: UniProt: A0A080S703, UniProt: Q5NEQ5*PLUS, ATP-polyphosphate phosphotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.8 M Na Citrate, 0.1 M Na HEPES, 2.5 mM AMP-PNP, 1 mM MgCl2

-
Data collection

DiffractionMean temperature: 273.15 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.23→81.65 Å / Num. obs: 61793 / % possible obs: 99.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.5
Reflection shellResolution: 2.23→2.29 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.539 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
BALBESphasing
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CZQ

3czq


Resolution: 2.23→76.638 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 3129 5.07 %
Rwork0.2029 --
obs0.2051 61720 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.23→76.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8502 0 0 383 8885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0148738
X-RAY DIFFRACTIONf_angle_d1.46411774
X-RAY DIFFRACTIONf_dihedral_angle_d15.213322
X-RAY DIFFRACTIONf_chiral_restr0.0491189
X-RAY DIFFRACTIONf_plane_restr0.0091525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.26490.33921580.30892600X-RAY DIFFRACTION100
2.2649-2.3020.34911230.27582692X-RAY DIFFRACTION100
2.302-2.34170.35771480.26492622X-RAY DIFFRACTION100
2.3417-2.38430.3451660.26262618X-RAY DIFFRACTION100
2.3843-2.43010.31861370.25422633X-RAY DIFFRACTION100
2.4301-2.47980.3221430.24862680X-RAY DIFFRACTION100
2.4798-2.53370.33321520.24182637X-RAY DIFFRACTION100
2.5337-2.59260.29371210.23092668X-RAY DIFFRACTION100
2.5926-2.65750.32311300.2372640X-RAY DIFFRACTION100
2.6575-2.72930.26741400.23292684X-RAY DIFFRACTION100
2.7293-2.80960.29651320.22962665X-RAY DIFFRACTION99
2.8096-2.90030.29151310.2282657X-RAY DIFFRACTION100
2.9003-3.0040.27491250.23452680X-RAY DIFFRACTION99
3.004-3.12430.26011560.22472657X-RAY DIFFRACTION100
3.1243-3.26640.26551400.20812682X-RAY DIFFRACTION99
3.2664-3.43870.25271440.22675X-RAY DIFFRACTION99
3.4387-3.65410.2471430.19652663X-RAY DIFFRACTION99
3.6541-3.93620.23081520.17712668X-RAY DIFFRACTION99
3.9362-4.33230.20941430.16382653X-RAY DIFFRACTION97
4.3323-4.95910.19211370.15532651X-RAY DIFFRACTION97
4.9591-6.24750.21911610.18842683X-RAY DIFFRACTION98
6.2475-76.68370.18161470.19792783X-RAY DIFFRACTION96

+
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