[English] 日本語
Yorodumi
- PDB-2kpm: Solution NMR Structure of uncharacterized protein from gene locus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kpm
TitleSolution NMR Structure of uncharacterized protein from gene locus NE0665 of Nitrosomonas europaea. Northeast Structural Genomics Target NeR103A
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / methods development / uncharacterized protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


RNA nuclease activity
Similarity search - Function
NYN domain, MARF1-type / NYN domain / LOTUS domain-like / OST-HTH/LOTUS domain / LOTUS-like domain / OST-HTH/LOTUS domain / OST-type HTH domain profile. / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HTH OST-type domain-containing protein
Similarity search - Component
Biological speciesNitrosomonas europaea (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model 1
AuthorsRossi, P. / Belote, R. / Jiang, M. / Xiao, R. / Ciccosanti, C. / Acton, T. / Everett, J. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of uncharacterized protein from gene locus NE0665 of Nitrosomonas europaea. Northeast Structural Genomics Target NeR103A
Authors: Rossi, P. / Xiao, R. / Acton, T. / Rost, B. / Montelione, G.T.
History
DepositionOct 16, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...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 1.3May 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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)11,9391
Polymers11,9391
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 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Uncharacterized protein


Mass: 11939.336 Da / Num. of mol.: 1 / Fragment: sequence database residues 174-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Gene: NE0665 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic / References: UniProt: Q82WK8

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D (H)CCH-TOCSY
1413D (H)CCH-COSY
1513D CCH-TOCSY
1613D HNCO
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D CBCA(CO)NH
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11213D HN(CA)CO
11313D HNCA
1142het-NOE
1152T1-pseudo2D
1162T2CPMG-pseudo2D
1172high-resC13-HSQC
11811D presat referencing
11911D presat referencing
NMR detailsText: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR. T1/T2(CPMG). CONSISTENT WITH MOLECULAR WEIGHT OF MONOMERIC UNIT.

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.957 mM [U-100% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.9 mM [U-5% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.957 mMprotein-1[U-100% 13C; U-100% 15N]1
200 mMsodium chloride-21
20 mMMES-31
10 mMDTT-41
0.02 %sodium azide-51
5 mMCalcium Chloride-61
50 uMDSS-71
0.9 mMprotein-8[U-5% 13C; U-100% 15N]2
200 mMsodium chloride-92
20 mMMES-102
10 mMDTT-112
0.02 %sodium azide-122
5 mMCalcium Chloride-132
50 uMDSS-142
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.112Goddarddata analysis
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
TALOS+Shen,Cornilescu, Delaglio and Baxgeometry optimization
PSVS1.3Bhattacharya and Montelionevalidation
TopSpin2.1Bruker Biospincollection
PyMOL1.2delano scientificvisualization
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
Details: Iterative noesy assignment followed by torsion angle dynamics in CYANA-3.0, STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA-3.0. 20 OF 100 STRUCTURES ...Details: Iterative noesy assignment followed by torsion angle dynamics in CYANA-3.0, STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA-3.0. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED WITH CYANA-3.0. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NILGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS (ALL RESIDUES INCLUDED): BACKBONE 86.63%, SIDECHAIN 76.84%, AROMATIC (SC) 100%, STEREOSPECIFIC VL METHYL ASSIGNMENT 100%, UNAMBIGUOUS SIDECHAIN NH2 100%. STRUCTURE BASED ON 2412 NOE, 230 DIHE. MAX NOE VIOLATION: 0.23 A (1MODEL); MAX DIHE VIOLATION: 8.1 DEG. 3 TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES: 19-98. SECONDARY STRUCTURE - ALPHA HELICES: 23-32, 42-52, 66-72. BETA STRANDS: 40-41, 90-96, 77-83. RMSD(ANG): BACKBONE 0.4, ALL HEAVY ATOMS 0.7. RAMA. DISTRIBUTION (MOLPROBITY): 97/3/0/0 PROCHECK (PSI-PHI): -0.12/-0.16 (RAW/Z), PROCHECK (ALL): 0.04/0.24 (RAW/Z), MOLPROBITY CLASH: 9.92/-0.18 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.91, PRECISION: 0.93, F-MEASURE: 0.92, DP-SCORE: 0.79.
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