[English] 日本語
Yorodumi
- PDB-2kj5: Solution NMR structure of a domain from a putative phage integras... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kj5
TitleSolution NMR structure of a domain from a putative phage integrase protein Nmul_A0064 from Nitrosospira multiformis, Northeast Structural Genomics Consortium Target NmR46C
ComponentsPhage integraseSite-specific recombination
KeywordsStructural Genomics / unknown function / phage integrase / GFT NMR / PSI-2 / NESG / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / DNA recombination / symbiont entry into host cell / DNA binding
Similarity search - Function
Integrase, DNA-binding domain / Integrase, DNA-binding domain superfamily / Arm DNA-binding domain / Tyrosine recombinase, N-terminal domain / Phage integrase family / Integrase, catalytic domain / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core / DNA polymerase; domain 1 ...Integrase, DNA-binding domain / Integrase, DNA-binding domain superfamily / Arm DNA-binding domain / Tyrosine recombinase, N-terminal domain / Phage integrase family / Integrase, catalytic domain / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesNitrosospira multiformis ATCC 25196 (bacteria)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsMills, J.L. / Eletsky, A. / Ghosh, A. / Wang, D. / Lee, H. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Swapna, G.V.T. ...Mills, J.L. / Eletsky, A. / Ghosh, A. / Wang, D. / Lee, H. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Swapna, G.V.T. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of a domain from a putative phage integrase protein Nmul_A0064 from Nitrosospira multiformis, Northeast Structural Genomics Consortium Target NmR46C.
Authors: Mills, J.L. / Eletsky, A. / Ghosh, A. / Wang, D. / Lee, H. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Swapna, G.V.T. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / ...Authors: Mills, J.L. / Eletsky, A. / Ghosh, A. / Wang, D. / Lee, H. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Swapna, G.V.T. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T.
History
DepositionMay 21, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2012Group: Database references / Structure summary
Revision 1.3Mar 14, 2012Group: Database references
Revision 1.4Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.5May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phage integrase


Theoretical massNumber of molelcules
Total (without water)13,4001
Polymers13,4001
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)20 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Phage integrase / Site-specific recombination


Mass: 13400.457 Da / Num. of mol.: 1 / Fragment: sequence database residues 101-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosospira multiformis ATCC 25196 (bacteria)
Gene: Nmul_A0064 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YCZ8

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1322D 1H-13C HSQC
1413D sim 15N,13C NOESY
1513D HNCO
161(4,3)D HNCABCA
171GFT (4,3)D CABCA(CO)NH
181GFT (4,3)D HABCAB(CO)NH
191GFT (4,3)D arom. (H)CCH
1101GFT (4,3)D aliph. (H)CCH
11132D 1H-15N HSQC
11232D 1H-15N TROSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-98% 13C; U-98% 15N] NmR46C, 10 % D2O, 90 % H2O, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 1x v/v protease inhibitors, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21.2 mM [U-5% 13C; U-98% 15N] NmR46C, 10 % D2O, 90 % H2O, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 1x v/v protease inhibitors, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31.2 mM [U-5% 13C; U-98% 15N] NmR46C, 10 % D2O, 90 % H2O, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 1x v/v protease inhibitors, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingSolution-ID
1.2 mMNmR46C-1[U-98% 13C; U-98% 15N]1
10 %D2O-21
90 %H2O-31
20 mMMES-41
200 mMsodium chloride-51
5 mMcalcium chloride-61
10 mMDTT-71
50 uMDSS-81
v/vprotease inhibitors-91
0.02 %sodium azide-101
1.2 mMNmR46C-11[U-5% 13C; U-98% 15N]2
10 %D2O-122
90 %H2O-132
20 mMMES-142
200 mMsodium chloride-152
5 mMcalcium chloride-162
10 mMDTT-172
50 uMDSS-182
v/vprotease inhibitors-192
0.02 %sodium azide-202
1.2 mMNmR46C-21[U-5% 13C; U-98% 15N]3
10 %D2O-223
90 %H2O-233
20 mMMES-243
200 mMsodium chloride-253
5 mMcalcium chloride-263
10 mMDTT-273
50 uMDSS-283
v/vprotease inhibitors-293
0.02 %sodium azide-303
Sample conditionsIonic strength: 430 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SPSCANGlaserprocessing
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
MOLMOLKoradi, Billeter and Wuthrichrefinement
MOLMOLKoradi, Billeter and Wuthrichstructure solution
AutoStructureHuang, Tejero, Powers and Montelionechemical shift assignment
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
AutoStructureHuang, Tejero, Powers and Montelionerefinement
PSVSBhattacharya and Montelionerefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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