[English] 日本語
Yorodumi
- PDB-2hep: Solution NMR structure of the UPF0291 protein ynzC from Bacillus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hep
TitleSolution NMR structure of the UPF0291 protein ynzC from Bacillus subtilis. Northeast Structural Genomics target SR384.
ComponentsUPF0291 protein ynzC
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SR384 / AUTOSTRUCTURE / Northeast Structural Genomics Consortium / PSI-1 / Protein Structure Initiative / NESG
Function / homologyProtein of unknown function DUF896 / Bacterial protein of unknown function (DUF896) / Helix hairpin bin / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / cytoplasm / UPF0291 protein YnzC
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsAramini, J.M. / Swapna, G.V.T. / Ho, C.K. / Shetty, K. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M. / Acton, T.B. ...Aramini, J.M. / Swapna, G.V.T. / Ho, C.K. / Shetty, K. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2008
Title: Solution NMR structure of the SOS response protein YnzC from Bacillus subtilis
Authors: Aramini, J.M. / Sharma, S. / Huang, Y.J. / Swapna, G.V. / Ho, C.K. / Shetty, K. / Cunningham, K. / Ma, L.C. / Zhao, L. / Owens, L.A. / Jiang, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T. ...Authors: Aramini, J.M. / Sharma, S. / Huang, Y.J. / Swapna, G.V. / Ho, C.K. / Shetty, K. / Cunningham, K. / Ma, L.C. / Zhao, L. / Owens, L.A. / Jiang, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T.
History
DepositionJun 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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: UPF0291 protein ynzC


Theoretical massNumber of molelcules
Total (without water)9,8951
Polymers9,8951
Non-polymers00
Water00
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 lowest conformational energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein UPF0291 protein ynzC


Mass: 9895.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ynzC / Plasmid: PET21, SR384-21.4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MGK / References: UniProt: O31818

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HNHA
1413D GFT-CBCACAcoNHN, GFT-HNNCACBCA, GFT-HABCAB(CO)NHN
1513D (H)CCH-TOCSY, CC(CO)NH TOCSY, (H)CCH-COSY
162high resolution 2D CH-HQSC (for stereospecific assignment of Val/Leu methyls)
1713D HNCO, HN(CA)CO
1812D 15N1H-heteronuclear NOE
NMR detailsText: The structure was determined using triple resonance NMR spectroscopy. AUTOASSIGN was used to obtain automatic backbone assignments from GFT peak lists. Side chain assignments were completed ...Text: The structure was determined using triple resonance NMR spectroscopy. AUTOASSIGN was used to obtain automatic backbone assignments from GFT peak lists. Side chain assignments were completed manually. Automatic NOESY assignment, as well as distance and hydrogen bond constraints were determined using AutoStructure. Dihedral angle constraints were determined using HYPER. Completeness of NMR assignments (excluding C-terminal LEHHHHHH tag): Backbone: 91.9%; Side chain: 78.3%; Aromatics, 100%: Stereospecific methyl, 87.5%. Final structure quality factors (for residues 1 to 42 only; PSVS 1.2), where ordered residues [S(PHI)+ S(PSI) > 1.8] comprise 5-20 and 23-40: (A) RMSD (ordered residues): BB, 0.9; heavy atom, 1.5. (B) Ramachandran statistics for ordered residues: Most favored, 96.4%, Additionally allowed, 3.6%, generously allowed, 0.0%, disallowed, 0.0%. (C) Procheck scores for ordered residues (Raw/Z-): PHI-PSI, 0.11/0.75; All, -0.12/-0.71. (D) Molprobity clash score (Raw/Z-): 14.69/-1.00. (E) RPF scores for goodness of fit to NOESY data (all residues): Recall, 0.952, Precision, 0.839, F-measure, 0.892, DP-score, 0.628

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.12mM U-13C,15N SR384, 20mM MES, 100mM NaCl, 5 mM CaCl2, 10mM DTT, 0.02% NaN3, pH 6.5, 5% D2O/95% H2O5% D2O/95% H2O
21.12mM 5%-13C,U-15N SR384, 20mM MES, 100mM NaCl, 5 mM CaCl2, 10mM DTT, 0.02% NaN3, pH 6.5, 5% D2O/95% H2O5% D2O/95% H2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 293 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AVANCEBrukerAVANCE6002

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
XwinNMR3.5pl6Brukercollection
AutoAssign2.2.1Zimmerman, Moseley, Montelionedata analysis
Sparky3.11Goddard & Knellerdata analysis
AutoStructure2.1.1Huang & Montelionerefinement
XPLOR-NIH2.11.2Clore et alrefinement
AGNuS2Moseley & Montelionedata analysis
PdbStat4.01Tejero & Montelionedata analysis
PSVS1.2Bhattacharya & Montelionedata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 403 conformationally restricting NOE-derived distance constraints, 67 dihedral angle constraints, 42 hydrogen bond constraints, and 29 J(HN-Halpha) ...Details: The structures are based on a total of 403 conformationally restricting NOE-derived distance constraints, 67 dihedral angle constraints, 42 hydrogen bond constraints, and 29 J(HN-Halpha) coupling constants (12.5 constraints per residue; 1.1 long range constraints per residue; computed for residues 1 to 42 by PSVS 1.2). Structure determination was performed iteratively using AutoStructure (XPLOR-NIH). A final XPLOR calculation using the final constraints derived from AutoStructure was performed to yield the final structures. The unstructured C-terminal half of the molecule was included in all structural calculations but has been omitted from this deposition. Heteronuclear 15N,1H NOE experiments corroborate the presence of significant disorder in the C-terminal half of the protein (residues 43 to C-terminus).
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with lowest conformational energy
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://pdbjlc1.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