[English] 日本語
Yorodumi
- PDB-7pvk: X-ray structure of dimeric PorX (T272A mutant), in complex with pGpG. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pvk
TitleX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.
Components
  • Response regulator
  • pGpG
KeywordsSIGNALING PROTEIN / Response regulator / Type 9 Secretion System / PglZ / Phosphodiesterase
Function / homology
Function and homology information


phosphorelay signal transduction system / metal ion binding
Similarity search - Function
PglZ domain / PglZ domain / Alkaline-phosphatase-like, core domain superfamily / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / FORMIC ACID / RNA / Response regulator
Similarity search - Component
Biological speciesPorphyromonas gingivalis W83 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsSchmitz, C.A. / Madej, M. / Potempa, J. / Sola, M.
Funding support Spain, Poland, 2items
OrganizationGrant numberCountry
Other government Spain
Other government Poland
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Response regulator PorX coordinates oligonucleotide signalling and gene expression to control the secretion of virulence factors
Authors: Schmitz, C. / Madej, M. / Nowakowska, Z. / Cuppari, A. / Jacula, A. / Ksiazek, M. / Mikruta, K. / Wisniewski, J. / Pudelko-Malik, N. / Saran, A. / Zeytuni, N. / Mlynarz, P. / Lamont, R.J. / ...Authors: Schmitz, C. / Madej, M. / Nowakowska, Z. / Cuppari, A. / Jacula, A. / Ksiazek, M. / Mikruta, K. / Wisniewski, J. / Pudelko-Malik, N. / Saran, A. / Zeytuni, N. / Mlynarz, P. / Lamont, R.J. / Uson, I. / Siksnys, V. / Potempa, J. / Sola, M.
History
DepositionOct 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 2.0Jan 4, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / refine / struct_asym / struct_conn / struct_ref / struct_ref_seq
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _refine.ls_percent_reflns_obs / _struct_asym.entity_id
Revision 2.1Jan 11, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Response regulator
B: Response regulator
C: Response regulator
D: Response regulator
E: pGpG
F: pGpG
G: pGpG
H: pGpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,89149
Polymers251,0078
Non-polymers2,88441
Water8,215456
1
A: Response regulator
B: Response regulator
E: pGpG
G: pGpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,05126
Polymers125,5044
Non-polymers1,54722
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11550 Å2
ΔGint-220 kcal/mol
Surface area41660 Å2
MethodPISA
2
C: Response regulator
D: Response regulator
F: pGpG
H: pGpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,84023
Polymers125,5044
Non-polymers1,33619
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10900 Å2
ΔGint-247 kcal/mol
Surface area41610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.630, 103.770, 132.210
Angle α, β, γ (deg.)90.000, 98.500, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / RNA chain , 2 types, 8 molecules ABCDEFGH

#1: Protein
Response regulator


Mass: 62106.418 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis W83 (bacteria)
Strain: ATCC BAA-308 / W83 / Gene: PG_0928 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7MVV4
#2: RNA chain
pGpG


Mass: 645.454 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 6 types, 497 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Glycine pH 8.5, 100 mM sodium formate, 3-4 % PEG 8 K, 15 mM MgCl2, 30 mM NaF, 5 mM BeSO4, 0.5 mM ZnCl2, 0.5 mM pGpG

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.4→51.9 Å / Num. obs: 98575 / % possible obs: 99.39 % / Redundancy: 14.4 % / Biso Wilson estimate: 65.79 Å2 / CC1/2: 0.999 / CC star: 1 / Rpim(I) all: 0.03333 / Net I/σ(I): 15.93
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 14.3 % / Num. unique obs: 9713 / CC1/2: 0.635 / CC star: 0.882 / Rpim(I) all: 0.9475 / % possible all: 98.28

-
Processing

Software
NameVersionClassification
PHENIX1.11.1refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→51.9 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.223 --
Rwork0.1937 --
obs-98355 99.39 %
Displacement parametersBiso max: 276.22 Å2 / Biso mean: 89.35 Å2 / Biso min: 44.67 Å2
Refinement stepCycle: LAST / Resolution: 2.4→51.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16940 0 343 456 17739

+
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