[English] 日本語
Yorodumi
- PDB-6fh1: Protein arginine kinase McsB in the apo state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fh1
TitleProtein arginine kinase McsB in the apo state
ComponentsProtein-arginine kinase
KeywordsSIGNALING PROTEIN / protein kinase / protein arginine kinase / protein arginine phosphorylation / phospho-binding domain
Function / homology
Function and homology information


protein arginine kinase / phosphocreatine biosynthetic process / creatine kinase activity / protein kinase activity / extracellular space / ATP binding
Similarity search - Function
Protein arginine kinase / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / Glutamine synthetase/guanido kinase, catalytic domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain ...Protein arginine kinase / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / Glutamine synthetase/guanido kinase, catalytic domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / IMIDAZOLE / Protein-arginine kinase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSuskiewicz, M.J. / Heuck, A. / Vu, L.D. / Clausen, T.
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Structure of McsB, a protein kinase for regulated arginine phosphorylation.
Authors: Suskiewicz, M.J. / Hajdusits, B. / Beveridge, R. / Heuck, A. / Vu, L.D. / Kurzbauer, R. / Hauer, K. / Thoeny, V. / Rumpel, K. / Mechtler, K. / Meinhart, A. / Clausen, T.
History
DepositionJan 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 17, 2024Group: 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: Protein-arginine kinase
B: Protein-arginine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,93425
Polymers82,5102
Non-polymers1,42423
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Native MS confirmed the dimeric assembly. Mutating the dimerisation interface (R273E) resulted in a monomer in native MS., light scattering, SEC-MALS confirmed the ...Evidence: mass spectrometry, Native MS confirmed the dimeric assembly. Mutating the dimerisation interface (R273E) resulted in a monomer in native MS., light scattering, SEC-MALS confirmed the dimeric assembly. Mutating the dimerisation interface (R273E) resulted in a monomer in SEC-MALS.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint61 kcal/mol
Surface area30070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.720, 83.410, 97.780
Angle α, β, γ (deg.)90.00, 98.90, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Protein-arginine kinase / protein arginine kinase McsB


Mass: 41255.207 Da / Num. of mol.: 2 / Mutation: delta356-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: mcsB / Plasmid: pET-21a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DMM5, protein arginine kinase
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 25% v/v ethylene glycol, 75 mM MES-imidazole, 58 mM sodium formate, 58 mM ammonium acetate, 58 mM sodium citrate, 58 mM sodium potassium tartrate, 58 mM sodium oxamate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 85408 / % possible obs: 95.93 % / Redundancy: 2.7 % / Biso Wilson estimate: 31.73 Å2 / Net I/σ(I): 13.47
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.6 % / Num. unique obs: 8509 / % possible all: 96.58

-
Processing

Software
NameVersionClassification
PHENIX(1.13rc1_2961: ???)refinement
Cootmodel building
Omodel building
ARP/wARPmodel building
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M15

1m15


Resolution: 1.7→42.954 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2000 2.36 %Random
Rwork0.194 ---
obs0.1947 84865 95.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→42.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5484 0 94 363 5941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075792
X-RAY DIFFRACTIONf_angle_d0.7537823
X-RAY DIFFRACTIONf_dihedral_angle_d18.4352229
X-RAY DIFFRACTIONf_chiral_restr0.056899
X-RAY DIFFRACTIONf_plane_restr0.0051026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74250.46181440.42215967X-RAY DIFFRACTION97
1.7425-1.78960.43091420.38945875X-RAY DIFFRACTION96
1.7896-1.84230.43231420.3695859X-RAY DIFFRACTION95
1.8423-1.90170.36371360.32165674X-RAY DIFFRACTION93
1.9017-1.96970.26731430.26445915X-RAY DIFFRACTION96
1.9697-2.04860.25071450.2196043X-RAY DIFFRACTION98
2.0486-2.14180.24791460.2166018X-RAY DIFFRACTION98
2.1418-2.25470.22651450.20496044X-RAY DIFFRACTION98
2.2547-2.3960.24171460.19726043X-RAY DIFFRACTION98
2.396-2.58090.23481450.20015995X-RAY DIFFRACTION97
2.5809-2.84060.23311430.1945900X-RAY DIFFRACTION96
2.8406-3.25160.21731380.1965755X-RAY DIFFRACTION93
3.2516-4.09610.21071390.16465739X-RAY DIFFRACTION92
4.0961-42.96790.16981460.15796038X-RAY DIFFRACTION96

+
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