[English] 日本語
Yorodumi
- PDB-8dx0: VanSC CA domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dx0
TitleVanSC CA domain
ComponentsHistidine kinase
KeywordsSIGNALING PROTEIN / ATP binding / histidine kinase
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / 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, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / 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 / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Biological speciesEnterococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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
DepositionAug 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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: Histidine kinase
B: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7185
Polymers34,6452
Non-polymers733
Water4,107228
1
A: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3472
Polymers17,3231
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3713
Polymers17,3231
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.700, 40.230, 64.710
Angle α, β, γ (deg.)90.000, 91.640, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Histidine kinase /


Mass: 17322.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus (bacteria) / Gene: vanSc / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KJT3, histidine kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 7
Details: Protein was concentrated to 2.5 mg/mL in 20 mM Tris pH 7.8, 150 mM NaCl supplemented with 2.5 mM AMP-PNP and 5 mM MgCl2. Protein and precipitant were mixed in a volume ratio of 1:3 and ...Details: Protein was concentrated to 2.5 mg/mL in 20 mM Tris pH 7.8, 150 mM NaCl supplemented with 2.5 mM AMP-PNP and 5 mM MgCl2. Protein and precipitant were mixed in a volume ratio of 1:3 and incubated under Als Oil at 277 K; the precipitant solution was 22% (w/v) PEG 6000, 100 mM HEPES buffer at pH 7.0. Crystals of comparable appearance and diffraction quality were obtained using MES buffer at pH 6.0, and Tris buffer at pH 8.0.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.45→64.7 Å / Num. obs: 55912 / % possible obs: 97.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 21.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.016 / Rrim(I) all: 0.039 / Net I/σ(I): 22.8
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.6 / Num. unique obs: 4842 / CC1/2: 0.682 / Rpim(I) all: 0.386 / Rrim(I) all: 0.718 / % possible all: 84.7

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Six models from SwissModel combined with Ensembler

Resolution: 1.45→34.16 Å / SU ML: 0.1662 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.1022 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2004 2729 4.88 %
Rwork0.1854 53160 -
obs0.1862 55889 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.09 Å2
Refinement stepCycle: LAST / Resolution: 1.45→34.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 3 228 2463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00962328
X-RAY DIFFRACTIONf_angle_d1.06763173
X-RAY DIFFRACTIONf_chiral_restr0.0913378
X-RAY DIFFRACTIONf_plane_restr0.0068411
X-RAY DIFFRACTIONf_dihedral_angle_d23.0416912
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.33111150.28352286X-RAY DIFFRACTION80.17
1.48-1.50.28981340.26192577X-RAY DIFFRACTION90.04
1.5-1.540.26341200.24092794X-RAY DIFFRACTION97.62
1.54-1.570.26251320.22262837X-RAY DIFFRACTION98.15
1.57-1.610.24021610.21282774X-RAY DIFFRACTION97.35
1.61-1.650.2231600.19482812X-RAY DIFFRACTION99.1
1.65-1.690.22411550.1912833X-RAY DIFFRACTION98.19
1.69-1.740.26211370.20082815X-RAY DIFFRACTION98.14
1.74-1.80.21041180.20342843X-RAY DIFFRACTION99.3
1.8-1.860.2481200.20152863X-RAY DIFFRACTION98.84
1.86-1.930.20611580.18362828X-RAY DIFFRACTION99.07
1.93-2.020.22421140.18582912X-RAY DIFFRACTION98.79
2.02-2.130.20111260.18732826X-RAY DIFFRACTION98.14
2.13-2.260.18161810.1782814X-RAY DIFFRACTION99.14
2.26-2.440.17981310.18572880X-RAY DIFFRACTION99.41
2.44-2.680.23591730.19122803X-RAY DIFFRACTION97.03
2.68-3.070.22031310.19622879X-RAY DIFFRACTION99.18
3.07-3.870.17731670.17392842X-RAY DIFFRACTION97.98
3.87-34.160.17661960.16692942X-RAY DIFFRACTION99.08
Refinement TLS params.Method: refined / Origin x: 17.04657852 Å / Origin y: 8.49773461621 Å / Origin z: 14.1315729981 Å
111213212223313233
T0.169872369928 Å20.0273954599045 Å20.000712615121355 Å2-0.186128439686 Å20.0152072397144 Å2--0.190709472354 Å2
L0.579368205052 °20.462751229036 °20.403961029788 °2-0.91218284393 °20.597767676252 °2--0.810859536441 °2
S-0.00624012244457 Å °-0.0468188630486 Å °-0.0401482725179 Å °0.0232816995512 Å °0.0346841756685 Å °-0.0714764466036 Å °0.00717971649002 Å °0.00180003929494 Å °-0.0302623333993 Å °
Refinement TLS groupSelection details: all

+
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