[English] 日本語
Yorodumi
- PDB-2jrm: Solution NMR structure of ribosome modulation factor VP1593 from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jrm
TitleSolution NMR structure of ribosome modulation factor VP1593 from Vibrio parahaemolyticus. Northeast Structural Genomics target VpR55
ComponentsRibosome modulation factor
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / solution NMR structure / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


regulation of translation / cytoplasm
Similarity search - Function
ribosome modulation factor like domain / Ribosome modulation factor / Ribosome modulation factor domain superfamily / Ribosome modulation factor / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ribosome modulation factor
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsTang, Y. / Rossi, P. / Swapna, G. / Wang, H. / Jiang, M. / Cunningham, K. / Owens, L. / Ma, L. / Xiao, R. / Liu, J. ...Tang, Y. / Rossi, P. / Swapna, G. / Wang, H. / Jiang, M. / Cunningham, K. / Owens, L. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Ribosome Modulation Factor VP1593 from Vibrio parahaemolyticus.
Authors: Tang, Y. / Rossi, P. / Swapna, G. / Wang, H. / Jiang, M. / Cunningham, K. / Owens, L. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T.
History
DepositionJun 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Dec 4, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Polymer sequence / Refinement description
Category: entity_poly / pdbx_database_related ...entity_poly / pdbx_database_related / pdbx_nmr_exptl_sample / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_refine / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _entity_poly.pdbx_target_identifier / _pdbx_nmr_exptl_sample.isotopic_labeling ..._entity_poly.pdbx_target_identifier / _pdbx_nmr_exptl_sample.isotopic_labeling / _pdbx_nmr_exptl_sample_conditions.temperature / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 2.1Dec 20, 2023Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.deposit_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribosome modulation factor


Theoretical massNumber of molelcules
Total (without water)7,8061
Polymers7,8061
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Ribosome modulation factor


Mass: 7805.653 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633
Description: The protein is a monomer by gel filtration chromatography and static light scattering.
Gene: VP1593 / Plasmid: VpR55-21.4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q87PC4

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D 1H-13C NOESY
1513D 1H-13C NOESY aromatic
1613D HNCO
1713D HN(CA)CB
1813D CBCA(CO)NH
1913D HBHA(CO)NH
11013D C(CO)NH
11113D (H)CCH-TOCSY
11213D CCH-TOCSY
11322D 1H-13C HSQC high resolution

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-100% 13C; U-100% 15N] VpR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3, 95% H2O/5% D2O95% H2O/5% D2O
21.1 mM [U-5% 13C; U-100% 15N] VpR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMVpR55[U-100% 13C; U-100% 15N]1
20 mMMESnatural abundance1
100 mMNaClnatural abundance1
5 mMCaCl2natural abundance1
10 mMDTTnatural abundance1
0.02 %NaN3natural abundance1
1.1 mMVpR55[U-5% 13C; U-100% 15N]2
20 mMMESnatural abundance2
100 mMNaClnatural abundance2
5 mMCaCl2natural abundance2
10 mMDTTnatural abundance2
0.02 %NaN3natural abundance2
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
AutoAssign2.2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
Sparky3.11Goddardpeak picking
Sparky3.11Goddarddata analysis
AutoStructure2.1.1Huang, Tejero, Powers and Montelionestructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIH2.11.2Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.11.2Schwieters, Kuszewski, Tjandra and Clorerefinement
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.3Bhattacharya and Montelionedata analysis
PdbStat4Tejero and Montelionepdb analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 10
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 865 COMFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 154 DIHEDRAL ANGLE CONSTRAINTS, AND 50 HYDROGEN BOND CONSTRAINTS (18.4 CONSTRAINTS ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 865 COMFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 154 DIHEDRAL ANGLE CONSTRAINTS, AND 50 HYDROGEN BOND CONSTRAINTS (18.4 CONSTRAINTS PER RESIDUE, 2.8 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 60 BY PSVS 1.3) STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR-NIH). AFTER A FINAL XPLOR CALCULATION USING THE CONSTRAINTS DERIVED FROM AUTOSTRUCTURE. THE 20 LOWEST ENERGY STRUCTURES OUT OF 100 WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYANMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). THE C-TERMINAL HIS TAG RESDIUES OF THE PROTEIN (HHHHH) WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED(S(PHI)+S(PSI)<1.8): 1-4, 54-60. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN AND THE SIDE CHAIN ASSIGNMENTS WERE CO PLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE, HIHEDRAL ANGLE (HYPER) AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. COMPLETENESS OF NMR ASSIGNMENT (EXCLUDING C-TERMINAL HHHHH): BACKBONE,99.66%, SIDE CHAIN, 92.20%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUE 1-60 PSVS 1.3), WHERE ORDERED RESIDUES (S(PHI)+S(PSI)>1.8) COMPRISE: 5-54. (A) RMSD (ORDERED RESIDUES): BB 0.5, HEAVY ATOM: 1.2 (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 83.6%, ADDITIONALLY ALLOWED: 13.8%, GENEROUSLY ALLOWED : 0.2%, DISALLOWED,2.3%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z): PHI-PSI, -0.14/-0.24, ALL , -0.16/-0.95. (D) MOLPROBITY CLASH SCORE (RAW/Z): 19.25/-1.78. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUE 1-60): RECALL, 0.962, PRECISION, 0.921, F-MEASURE, 0.941, DP-SCORE, 0.804.
NMR constraintsNOE constraints total: 865 / NOE intraresidue total count: 171 / NOE long range total count: 164 / NOE medium range total count: 277 / NOE sequential total count: 253
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 4.9 ° / Maximum upper distance constraint violation: 0.45 Å
NMR ensemble rmsDistance rms dev: 0.02 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