[English] 日本語
Yorodumi
- PDB-1ckv: STRUCTURE OF THE SOLUBLE METHANE MONOOXYGENASE REGULATORY PROTEIN B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ckv
TitleSTRUCTURE OF THE SOLUBLE METHANE MONOOXYGENASE REGULATORY PROTEIN B
ComponentsPROTEIN (PROTEIN B)
KeywordsHYDROXYLASE REGULATORY PROTEIN
Function / homology
Function and homology information


cellular aromatic compound metabolic process / monooxygenase activity
Similarity search - Function
Monooxygenase component MmoB/DmpM / Phenol Hydroxylase P2 Protein / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Methane monooxygenase regulatory protein B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsWalters, K.J. / Gassner, G.T. / Lippard, S.J. / Wagner, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Structure of the soluble methane monooxygenase regulatory protein B.
Authors: Walters, K.J. / Gassner, G.T. / Lippard, S.J. / Wagner, G.
History
DepositionApr 25, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 7, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (PROTEIN B)


Theoretical massNumber of molelcules
Total (without water)16,0001
Polymers16,0001
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 20NO NOE VIOLOTION GREATER THAN 0.5 ANGSTROMS AND NO DIHEDRAL ANGLE VIOLATION GREATER THAN 5 DEGREES.
Representative

-
Components

#1: Protein PROTEIN (PROTEIN B)


Mass: 15999.864 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P18797

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCO
121HN(CA)CO
131HNCA
141HN(CO)CA
151HNHA
161(H)CCH-TOCSY
171HC(CO)NH
181H(CCO)NH
191HNHB
1101HNHA
1111NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 3D HETERONUCLEAR AND 2D HOMONUCLEAR NMR SPECTROSCOPY.

-
Sample preparation

DetailsContents: 4 MM PEFAPLOC
Sample conditionsIonic strength: 50 mM PHOSPHATE / pH: 6.5 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian DMX600VarianDMX6007501
Bruker INOVA750BrukerINOVA7506002
Bruker U500BrukerU5005003
Bruker INOVA500BrukerINOVA5005004

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
Felixstructure solution
EASYstructure solution
TALOSstructure solution
XPLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: NO NOE VIOLOTION GREATER THAN 0.5 ANGSTROMS AND NO DIHEDRAL ANGLE VIOLATION GREATER THAN 5 DEGREES.
Conformers calculated total number: 20 / Conformers submitted total number: 14

+
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