[English] 日本語
Yorodumi
- PDB-5tqj: Crystal structure of response regulator receiver protein from Bur... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tqj
TitleCrystal structure of response regulator receiver protein from Burkholderia phymatum
ComponentsResponse regulator receiver protein
KeywordsSIGNALING PROTEIN / Burkholderia phymatum / regulator / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


phosphorelay signal transduction system
Similarity search - Function
: / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Response regulator receiver protein
Similarity search - Component
Biological speciesBurkholderia phymatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsEdwards, T.E. / Dranow, D.M. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of response regulator receiver protein from Burkholderia phymatum
Authors: Edwards, T.E. / Dranow, D.M. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionOct 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Structure summary
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Response regulator receiver protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7715
Polymers14,6031
Non-polymers1684
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.600, 82.600, 31.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-429-

HOH

-
Components

#1: Protein Response regulator receiver protein


Mass: 14602.733 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia phymatum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: B2JEF9
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: BuphA.00051.a.B1.PS38011 at 14 mg/mL against MCSG1 screen condition C9, 0.8M LiCl, 0.1 M Tris pH 8.5, 32% PEG 4000 supplemented with 20% ethylene glycol as cryo protectant, crystal tracking ...Details: BuphA.00051.a.B1.PS38011 at 14 mg/mL against MCSG1 screen condition C9, 0.8M LiCl, 0.1 M Tris pH 8.5, 32% PEG 4000 supplemented with 20% ethylene glycol as cryo protectant, crystal tracking ID 284229c9, unique puck LBQ7-6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 26700 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Biso Wilson estimate: 9.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Net I/σ(I): 25.89
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.3-1.330.4166.30.955191.7
1.33-1.370.357.50.968195.5
1.37-1.410.3058.530.976193.1
1.41-1.450.25510.080.983194.1
1.45-1.50.20512.530.989195.3
1.5-1.550.1615.520.991195
1.55-1.610.1417.550.994195.7
1.61-1.680.11920.240.996194.7
1.68-1.750.09724.240.997196.6
1.75-1.840.08227.470.998197.1
1.84-1.940.06932.610.998196.9
1.94-2.060.05937.390.998196.7
2.06-2.20.05141.910.999197.1
2.2-2.370.04745.350.999197.6
2.37-2.60.04448.120.999198.1
2.6-2.910.04350.720.999197.2
2.91-3.360.04154.090.999199.1
3.36-4.110.0455.790.997198.5
4.11-5.810.03955.390.999198.9
5.81-500.0450.870.999196.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIX1.11rc3_2553refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NHZ

3nhz


Resolution: 1.3→36.94 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 14.98
RfactorNum. reflection% reflection
Rfree0.1715 2012 7.55 %
Rwork0.1384 --
obs0.1409 26662 95.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.95 Å2 / Biso mean: 14.208 Å2 / Biso min: 5.94 Å2
Refinement stepCycle: final / Resolution: 1.3→36.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms919 0 7 168 1094
Biso mean--32.05 26.3 -
Num. residues----124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005996
X-RAY DIFFRACTIONf_angle_d0.8451373
X-RAY DIFFRACTIONf_chiral_restr0.075167
X-RAY DIFFRACTIONf_plane_restr0.005183
X-RAY DIFFRACTIONf_dihedral_angle_d16.926378
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.33260.19861240.15771675179992
1.3326-1.36860.23141210.15111721184296
1.3686-1.40890.20981330.14821690182393
1.4089-1.45430.20121610.14061703186494
1.4543-1.50630.15711610.13341666182795
1.5063-1.56660.18241450.13051705185095
1.5666-1.63790.17181400.12881757189796
1.6379-1.72430.18411310.13211749188096
1.7243-1.83230.16161300.1261783191396
1.8323-1.97380.13451160.12751812192896
1.9738-2.17240.1461670.1251758192597
2.1724-2.48670.15471610.13781810197198
2.4867-3.13270.18761550.1471851200699
3.1327-36.95470.1741670.14531970213799

+
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