[English] 日本語
Yorodumi
- PDB-8dvq: CA domain of VanSA histidine kinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dvq
TitleCA domain of VanSA histidine kinase
ComponentsSensor protein VanS
KeywordsSIGNALING PROTEIN / ATP-binding / histidine kinase
Function / homology
Function and homology information


cellular response to phosphate starvation / phosphorelay sensor kinase activity / histidine kinase / phosphoprotein phosphatase activity / negative regulation of DNA-binding transcription factor activity / cell wall organization / response to antibiotic / ATP binding / plasma membrane
Similarity search - Function
: / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
: / Sensor protein VanS
Similarity search - Component
Biological speciesEnterococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.19 Å
AuthorsLoll, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI148679 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structure of VanS from vancomycin-resistant enterococci: A sensor kinase with weak ATP binding.
Authors: Grasty, K.C. / Guzik, C. / D'Lauro, E.J. / Padrick, S.B. / Beld, J. / Loll, P.J.
History
DepositionJul 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sensor protein VanS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4803
Polymers18,2561
Non-polymers2252
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.830, 94.400, 29.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

-
Components

#1: Protein Sensor protein VanS / Vancomycin histidine protein kinase / Vancomycin resistance protein VanS


Mass: 18255.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus (bacteria) / Gene: vanS / Plasmid: pETHSUL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06240, histidine kinase
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 8.2
Details: Protein and precipitant were mixed in a volume ratio of 1:2 and incubated under Als Oil at 291K; the precipitant solution was obtained from the Berkeley Screen and contained 75 mM Bis-Tris ...Details: Protein and precipitant were mixed in a volume ratio of 1:2 and incubated under Als Oil at 291K; the precipitant solution was obtained from the Berkeley Screen and contained 75 mM Bis-Tris Propane, 25 mM citric acid, pH 8.2, 20 mM CdCl2, and 25 (w-v) PEG 400.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92009 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92009 Å / Relative weight: 1
ReflectionResolution: 2.19→28.7 Å / Num. obs: 10676 / % possible obs: 99.7 % / Redundancy: 8.55 % / Biso Wilson estimate: 43.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.033 / Rrim(I) all: 0.096 / Net I/σ(I): 13
Reflection shellResolution: 2.19→2.27 Å / Num. unique obs: 1031 / CC1/2: 0.849 / % possible all: 98

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIX1.14_3260phasing
RefinementMethod to determine structure: SAD / Resolution: 2.19→28.69 Å / SU ML: 0.1943 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.4862 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2362 533 5.02 %
Rwork0.1897 10088 -
obs0.192 10621 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63 Å2
Refinement stepCycle: LAST / Resolution: 2.19→28.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1015 0 2 45 1062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01141033
X-RAY DIFFRACTIONf_angle_d1.26131400
X-RAY DIFFRACTIONf_chiral_restr0.0721162
X-RAY DIFFRACTIONf_plane_restr0.0062181
X-RAY DIFFRACTIONf_dihedral_angle_d3.7566619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.410.29161300.23952450X-RAY DIFFRACTION99.04
2.41-2.760.29741330.20572481X-RAY DIFFRACTION99.77
2.76-3.480.251330.21972502X-RAY DIFFRACTION99.55
3.48-28.690.21221370.16712655X-RAY DIFFRACTION99.57
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)
14.83124152728-0.374872421975-2.17112189312.471500532210.4904284635744.66301367010.0657759289103-0.084039209912-0.155006149106-0.04223041629710.08645781531090.06960610348290.097820319406-0.0142221317141-0.1051029545340.2715414821070.00323465745488-0.04721142304710.450490206737-0.0148034339680.27324043270840.68615.13812.781
24.33811096664E-1102.2299911772E-133.75814505167E-1203.84115306345E-113596.37996069-152660.128719-1399242.78689-8.3018064856E-8-4.97755578484E-7-60608.838681117733.04478-35129.2758823-3596.379960190.525155533325-0.0829376151293-0.01021163275930.9827494926330.1229603759110.56599637925257.86524.6168.917
39.16732247575E-11-6.47466404143E-12-6.47466404073E-127.74874509637E-117.12088632253E-117.12088632253E-11104419.0320071920241.006521036647.35999-1733725.30126-146335.46053541916.4285225-1531211.61103-146335.46052341916.42852750.7001333783080.0930235634667-0.05188703866340.792400289519-0.02281897180150.49320841248746.8820.16526.074
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:157 )A9 - 157
2X-RAY DIFFRACTION2( CHAIN A AND RESID 201:201 )A201
3X-RAY DIFFRACTION3( CHAIN A AND RESID 202:202 )A202

+
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