[English] 日本語
Yorodumi
- PDB-2jmp: Structure for the N-terminus of chromosomal replication initiatio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jmp
TitleStructure for the N-terminus of chromosomal replication initiation protein dnaA from M. genitalium
ComponentsChromosomal replication initiator protein dnaA
KeywordsDNA BINDING PROTEIN / N-terminal / protein / Structural Genomics / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC
Function / homology
Function and homology information


regulation of DNA replication / DNA replication origin binding / DNA replication initiation / DNA replication / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
DnaA N-terminal domain / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Chromosomal replication control, initiator DnaA, conserved site / Bacterial dnaA protein helix-turn-helix / DnaA protein signature. / Bacterial dnaA protein helix-turn-helix domain / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial DnaA ATPAse domain ...DnaA N-terminal domain / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Chromosomal replication control, initiator DnaA, conserved site / Bacterial dnaA protein helix-turn-helix / DnaA protein signature. / Bacterial dnaA protein helix-turn-helix domain / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial DnaA ATPAse domain / Trp repressor/replication initiator / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chromosomal replication initiator protein DnaA
Similarity search - Component
Biological speciesMycoplasma genitalium (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLowery, T.J. / Pelton, J.G. / Wemmer, D.E. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: J.Struct.Funct.Genom. / Year: 2007
Title: NMR structure of the N-terminal domain of the replication initiator protein DnaA.
Authors: Lowery, T.J. / Pelton, J.G. / Chandonia, J.M. / Kim, R. / Yokota, H. / Wemmer, D.E.
History
DepositionNov 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.6May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chromosomal replication initiator protein dnaA


Theoretical massNumber of molelcules
Total (without water)12,3441
Polymers12,3441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Chromosomal replication initiator protein dnaA


Mass: 12343.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma genitalium (bacteria) / Gene: dnaA / Production host: Escherichia coli (E. coli) / References: UniProt: P35888

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HNCA
1323D CBCA(CO)NH
1423D HN(CA)CB
1523D HNCO
1623D C(CO)NH
1723d HN(CA)CO
1813D HNHA
1923D HN(CA)CO
11023D H(CCO)NH
11113D 1H-15N TOCSY
11223D (H)CCH-TOCSY
11323D H(CCO)NH
11423D HBHA(CO)NH
11513D 1H-15N NOESY
11613D HNHA
11743D 1H-13C NOESY
11843D 1H-13C NOESY
11944D (H)CCH NOESY
12052D 1H-13C HSQC
12132D 1H-1H NOESY
12232D DQF-COSY
12332D 1H-1H TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.75 mM [U-100% 15N] N_dnaA, 50 mM sodium phosphate, 100 mM sodium chloride, 2 mM EDTA, 0.05 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.75 mM [U-98% 13C; U-98% 15N] N_dnaA, 50 mM sodium phosphate, 100 mM sodium chloride, 2 mM EDTA, 0.05 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.75 mM N_dnaA, 50 mM sodium phosphate, 100 mM sodium chloride, 2 mM EDTA, 0.05 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
40.75 mM [U-98% 13C; U-98% 15N] N_dnaA, 50 mM sodium phosphate, 100 mM sodium chloride, 2 mM EDTA, 0.05 % sodium azide, 100% D2O100% D2O
50.75 mM 10% 13C-labeled N_dnaA, 50 mM sodium phosphate, 100 mM sodium chloride, 2 mM EDTA, 0.05 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.75 mMN_dnaA[U-100% 15N]1
50 mMsodium phosphate1
100 mMsodium chloride1
2 mMEDTA1
0.05 %sodium azide1
0.75 mMN_dnaA[U-98% 13C; U-98% 15N]2
50 mMsodium phosphate2
100 mMsodium chloride2
2 mMEDTA2
0.05 %sodium azide2
0.75 mMN_dnaA3
50 mMsodium phosphate3
100 mMsodium chloride3
2 mMEDTA3
0.05 %sodium azide3
0.75 mMN_dnaA[U-98% 13C; U-98% 15N]4
50 mMsodium phosphate4
100 mMsodium chloride4
2 mMEDTA4
0.05 %sodium azide4
0.75 mMN_dnaA10% 13C-labeled5
50 mMsodium phosphate5
100 mMsodium chloride5
2 mMEDTA5
0.05 %sodium azide5
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DMXBrukerDMX6002
Bruker AvanceBrukerAVANCE8003
Bruker AvanceBrukerAVANCE9004

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipe2.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CARA1.5.5Rochus Keller & Datonal AGchemical shift assignment
X-PLOR NIH2.11.2Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.11.2Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Structures were calculated starting from random coordinates. Starting structures were subjected to 2000 steps of high temp (50,000 K) torsion-angle simulated annealing, followed by 2000 ...Details: Structures were calculated starting from random coordinates. Starting structures were subjected to 2000 steps of high temp (50,000 K) torsion-angle simulated annealing, followed by 2000 torsion angle-based cooling steps, 2000 cartesian-based cooling steps, and 1000 steps of Powell energy minimization.
NMR constraintsNOE constraints total: 742 / NOE intraresidue total count: 286 / NOE long range total count: 159 / NOE medium range total count: 103 / NOE sequential total count: 194 / Hydrogen bond constraints total count: 50 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 46 / Protein psi angle constraints total count: 0
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 3.9 ° / Maximum upper distance constraint violation: 0.26 Å
NMR ensemble rmsDistance rms dev: 0.014 Å / Distance rms dev error: 0.002 Å

+
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