[English] 日本語
Yorodumi
- PDB-6vve: Legionella pneumophila Lpg2603 kinase bound to IP6, Mn2+, and ADP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vve
TitleLegionella pneumophila Lpg2603 kinase bound to IP6, Mn2+, and ADP
ComponentsDot/Icm T4SS effector
KeywordsTRANSFERASE / phosphorylation / kinase / IP6 / ADP
Function / homology
Function and homology information


host cell cytoplasmic vesicle / regulation of GTPase activity / small GTPase binding / nucleotide binding
Similarity search - Function
DrrA phosphatidylinositol 4-phosphate binding domain / DrrA, PI4P binding domain superfamily / DrrA phosphatidylinositol 4-phosphate binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / Dot/Icm T4SS effector / DrrA phosphatidylinositol 4-phosphate binding domain-containing protein
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTomchick, D.R. / Tagliabracci, V.S. / Park, B.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R00DK099254 United States
Welch FoundationI-1911 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: ALegionellaeffector kinase is activated by host inositol hexakisphosphate.
Authors: Sreelatha, A. / Nolan, C. / Park, B.C. / Pawlowski, K. / Tomchick, D.R. / Tagliabracci, V.S.
History
DepositionFeb 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Oct 14, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Oct 11, 2023Group: 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
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dot/Icm T4SS effector
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6514
Polymers36,5091
Non-polymers1,1423
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-14 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.535, 77.073, 72.557
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-659-

HOH

-
Components

#1: Protein Dot/Icm T4SS effector / Lpg2603


Mass: 36508.906 Da / Num. of mol.: 1 / Fragment: UNP residues 21-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_13135, DI056_05180, DI105_03620 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6F2W2, UniProt: Q5ZSB6*PLUS
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.03 Å3/Da / Density % sol: 39.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1 M citric acid, 7% MKPD, 0.03 M sodium chloride, 0.5 mM IP6, 1 mM manganese chloride, 1 mM APS-PNP, 35% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5414 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 19, 2019
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5414 Å / Relative weight: 1
ReflectionResolution: 1.77→29.85 Å / Num. obs: 22536 / % possible obs: 76.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 18.83 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.066 / Net I/σ(I): 14.9
Reflection shellResolution: 1.77→1.97 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2259 / Rpim(I) all: 0.395 / % possible all: 29

-
Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6VVC

6vvc


Resolution: 1.85→29.85 Å / SU ML: 0.2609 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.3101
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 1036 4.7 %random
Rwork0.2095 21001 --
obs0.2108 22037 85.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.11 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 64 162 2630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00462545
X-RAY DIFFRACTIONf_angle_d0.63793463
X-RAY DIFFRACTIONf_chiral_restr0.0416350
X-RAY DIFFRACTIONf_plane_restr0.0036436
X-RAY DIFFRACTIONf_dihedral_angle_d14.0417958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.950.3561710.32931365X-RAY DIFFRACTION39.52
1.95-2.070.33741090.28712439X-RAY DIFFRACTION70.21
2.07-2.230.28151390.25063011X-RAY DIFFRACTION86.97
2.23-2.450.31361530.2263469X-RAY DIFFRACTION99.1
2.45-2.810.25091840.20693497X-RAY DIFFRACTION100
2.81-3.540.20991850.18333535X-RAY DIFFRACTION100
3.54-29.850.18861950.18673685X-RAY DIFFRACTION99.87
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)
14.09542832704-0.4887651771180.4072946867752.157871524680.4992718945033.25343795948-0.179234684685-0.1576923498380.4085204820360.06606168933250.0613076554881-0.0577957404632-0.2626201337030.152839623310.01234271842850.172235027689-0.023898128822-0.02190710275010.13822236584-0.08435234538330.16796545769524.916340783323.206406685726.3295870069
21.71260261812-0.0006507739489631.04514712611.643509576141.230657341992.55262587223-0.0862354645041-0.1332384753650.2149007347390.0313665132253-0.00494909657090.232550518771-0.129149387137-0.1024283357240.0418166488290.0949661332089-0.01562231970840.01302656072540.09380195990020.003514973702330.1269719212514.373530321515.617398005417.2955432165
32.78211244833-0.9045809467871.356024774624.58370325016-2.57693356513.30699032601-0.0682629150527-0.0390329903226-0.2795480796960.04665796334580.1991480038450.1703542894470.102293524015-0.054553153449-0.09576390889090.05278619710380.000272682803492-0.0002184513950040.1211843401960.00953770757540.11083440613117.0393600235-3.1810029255316.0066006519
42.39716994917-0.294884434426-0.2980253941243.750621678810.4316491882162.23761955523-0.05786904506840.5475977817750.0358749047599-0.2596110141540.0310847067-0.09930375261670.06491572486220.2880419066350.02913167861020.1174008607-0.0281744921394-0.02514322173920.2312357817220.006530404689710.098818086833112.75402971951.35455303225-4.04896502772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 228 )
3X-RAY DIFFRACTION3chain 'A' and (resid 229 through 249 )
4X-RAY DIFFRACTION4chain 'A' and (resid 250 through 320 )

+
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://pdbjlvh1.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