[English] 日本語
Yorodumi
- PDB-2nt3: Receiver domain from Myxococcus xanthus social motility protein F... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nt3
TitleReceiver domain from Myxococcus xanthus social motility protein FrzS (Y102A Mutant)
ComponentsResponse regulator homolog
KeywordsSIGNALING PROTEIN / social motility / receiver domain / signalling
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 homolog
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsFraser, J.S. / Echols, N. / Merlie, J.P. / Zusman, D.R. / Alber, T.
CitationJournal: Mol.Microbiol. / Year: 2007
Title: An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS.
Authors: Fraser, J.S. / Merlie, J.P. / Echols, N. / Weisfield, S.R. / Mignot, T. / Wemmer, D.E. / Zusman, D.R. / Alber, T.
History
DepositionNov 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 27, 2012Group: Structure summary
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: 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: Response regulator homolog


Theoretical massNumber of molelcules
Total (without water)13,5941
Polymers13,5941
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.804, 63.804, 46.738
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-308-

HOH

-
Components

#1: Protein Response regulator homolog


Mass: 13594.427 Da / Num. of mol.: 1 / Fragment: Receiver domain / Mutation: Y102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: frzS / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21+ / References: UniProt: O68522
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.02 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 0.1M MIB buffer pH 7.0, 25% w/v PEG 1500, VAPOR DIFFUSION, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. all: 26709 / Num. obs: 26709 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 12.057 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 12
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 2.7 / Num. unique all: 28578 / Rsym value: 0.837 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2gkg

2gkg


Resolution: 1.3→20 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.555 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.049 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16244 1387 5.2 %RANDOM
Rwork0.13191 ---
all0.13352 25322 --
obs0.13352 25322 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.977 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.1 Å20 Å2
2--0.21 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 0 211 1121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022985
X-RAY DIFFRACTIONr_bond_other_d0.0070.02931
X-RAY DIFFRACTIONr_angle_refined_deg1.591.9781345
X-RAY DIFFRACTIONr_angle_other_deg0.88232164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8285135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.63824.77344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.54315169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.645158
X-RAY DIFFRACTIONr_chiral_restr0.1070.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021153
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02187
X-RAY DIFFRACTIONr_nbd_refined0.2340.2206
X-RAY DIFFRACTIONr_nbd_other0.1930.2976
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2507
X-RAY DIFFRACTIONr_nbtor_other0.0860.2643
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2132
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2150.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.237
X-RAY DIFFRACTIONr_mcbond_it1.7871.5853
X-RAY DIFFRACTIONr_mcbond_other0.6351.5266
X-RAY DIFFRACTIONr_mcangle_it2.15821041
X-RAY DIFFRACTIONr_scbond_it2.93392
X-RAY DIFFRACTIONr_scangle_it3.6534.5304
X-RAY DIFFRACTIONr_rigid_bond_restr1.41232268
X-RAY DIFFRACTIONr_sphericity_free7.7553211
X-RAY DIFFRACTIONr_sphericity_bonded2.81331898
LS refinement shellResolution: 1.3→1.37 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.216 218 -
Rwork0.173 3622 -
obs--99.9 %

+
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