[English] 日本語
Yorodumi
- PDB-2ezk: SOLUTION NMR STRUCTURE OF THE IBETA SUBDOMAIN OF THE MU END DNA B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ezk
TitleSOLUTION NMR STRUCTURE OF THE IBETA SUBDOMAIN OF THE MU END DNA BINDING DOMAIN OF PHAGE MU TRANSPOSASE, REGULARIZED MEAN STRUCTURE
ComponentsTRANSPOSASE
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / TRANSPOSITION / TRANSPOSABLE ELEMENT
Function / homology
Function and homology information


Ligases; Forming phosphoric-ester bonds / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / latency-replication decision / transposase activity / DNA transposition / double-stranded DNA endonuclease activity / viral DNA genome replication / ligase activity / DNA integration / DNA replication ...Ligases; Forming phosphoric-ester bonds / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / latency-replication decision / transposase activity / DNA transposition / double-stranded DNA endonuclease activity / viral DNA genome replication / ligase activity / DNA integration / DNA replication / host cell cytoplasm / DNA repair / DNA binding / metal ion binding
Similarity search - Function
Bacteriophage Mu, transposase / Transposase, Mu, C-terminal / Mu DNA binding, I gamma subdomain / Transposase-like, Mu, C-terminal / Bacteriophage Mu transposase / Mu DNA binding, I gamma subdomain / Mu transposase, C-terminal / Mu-type HTH domain / Mu DNA-binding domain / Mu-type HTH domain profile. ...Bacteriophage Mu, transposase / Transposase, Mu, C-terminal / Mu DNA binding, I gamma subdomain / Transposase-like, Mu, C-terminal / Bacteriophage Mu transposase / Mu DNA binding, I gamma subdomain / Mu transposase, C-terminal / Mu-type HTH domain / Mu DNA-binding domain / Mu-type HTH domain profile. / Putative DNA-binding domain superfamily / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage Mu (virus)
MethodSOLUTION NMR / simulated annealing
AuthorsClore, G.M. / Clubb, R.T. / Schumaker, S. / Gronenborn, A.M.
CitationJournal: EMBO J. / Year: 1997
Title: Solution structure of the Mu end DNA-binding ibeta subdomain of phage Mu transposase: modular DNA recognition by two tethered domains.
Authors: Schumacher, S. / Clubb, R.T. / Cai, M. / Mizuuchi, K. / Clore, G.M. / Gronenborn, A.M.
History
DepositionOct 4, 1997Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_keywords.text
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSPOSASE


Theoretical massNumber of molelcules
Total (without water)11,1861
Polymers11,1861
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)1 / 29REGULARIZED MEAN STRUCTURE
Representative

-
Components

#1: Protein TRANSPOSASE /


Mass: 11186.460 Da / Num. of mol.: 1 / Fragment: IBETA SUBDOMAIN, RESIDUES 77 - 174 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage Mu (virus) / Genus: Mu-like viruses / References: UniProt: P07636

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN: CBCA(CO)NH
121CBCANH
131HBHA(CO)NH
141C(CO)NH
151H(CCO)NH
161(H)CCH-COSY
171(H)CCH-TOCSY
181HNHA
19115N-SEPARATED HOHAHA; QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS; 3D 15N-SEPARATED NOE
11013D 13C-SEPARATED NOE AND ROE
11114D 15N/13C-SEPARATED NOE
11214D 13C/13C-SEPARATED NOE EXPERIMENTS

-
Sample preparation

Sample conditionspH: 6.3 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX500BrukerAMX5005001
Bruker AMX600BrukerAMX6006002

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionClassification
X-PLOR (SEE ABOVE)ABOVE)structure solution
X-PLOR (SEE ABOVE)ABOVE)refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE 3D STRUCTURE OF THE IBETA SUBDOMAIN OF MU A TRANSPOSASE WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR NMR AND IS BASED ON 1446 EXPERIMENTAL NMR RESTRAINTS: 255 SEQUENTIAL (|I- J|=1), 220 ...Details: THE 3D STRUCTURE OF THE IBETA SUBDOMAIN OF MU A TRANSPOSASE WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR NMR AND IS BASED ON 1446 EXPERIMENTAL NMR RESTRAINTS: 255 SEQUENTIAL (|I- J|=1), 220 MEDIUM RANGE (1 < |I-J| <=5) AND 252 LONG RANGE (|I-J| >5) INTERRESIDUES AND 234 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; 52 DISTANCE RESTRAINTS FOR 26 BACKBONE H-BONDS;. 153 TORSION ANGLE RESTRAINTS (94 PHI, 8 PSI, 36 CHI1 AND 15 CHI2); 58 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; AND 180 (92 CALPHA AND 88 CBETA) 13C SHIFT RESTRAINTS. THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J. MAGN. RESON. SERIES B 104, 99-103) AND CARBON CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92-96) RESTRAINTS, AND A CONFORMATIONAL DATABASE POTENTIAL (KUSZEWSKI ET AL.(1996) PROTEIN SCI. 5, 1067-1080; KUSZEWSKI ET AL. (1997) J. MAGN. RESON 125, 171-177). THE RESTRAINED REGULARIZED MEAN STRUCTURE IS PRESENTED IN ENTRY 2EZK AND 29 STRUCTURES ARE PRESENTED IN ENTRY 2EZL, AND THE EXPERIMENTAL RESTRAINTS IN R2EZKMR. IN THE RESTRAINED REGULARIZED MEAN COORDINATES (2EZK) THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS. THE LAST COLUMN IN THE INDIVIDUAL SA THE STRUCTURES (2EZI) HAS NO MEANING. BEST FITTING TO GENERATE AVERAGE STRUCTURE IS WITH RESPECT TO RESIDUES 89 - 166. RESIDUES 76 - 88 AND 167 - 174 AT THE N- AND C-TERMINI ARE POORLY DEFINED BY THE EXPERIMENTAL DATA. NOTE THE OCCUPANCY FIELD HAS NO MEANING. RMSD IN BONDS,ANGLES,IMPROPERS,CDIH,NOE,COUP: 2808E-03,0.871524,1.02906,0.295155,2.337017E-02,0.902726 SHIFTS RMS A, B: 1.04343, 1.11143
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers calculated total number: 29 / Conformers submitted total number: 1

+
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