[English] 日本語
Yorodumi
- PDB-2ki8: Solution NMR structure of tungsten formylmethanofuran dehydrogena... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ki8
TitleSolution NMR structure of tungsten formylmethanofuran dehydrogenase subunit D from Archaeoglobus fulgidus, Northeast Structural Genomics Consortium target AtT7
ComponentsTungsten formylmethanofuran dehydrogenase, subunit D (FwdD-2)
KeywordsOXIDOREDUCTASE / beta-barrel / FwdD-2 / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


molybdopterin cofactor binding / oxidoreductase activity
Similarity search - Function
Formylmethanofuran dehydrogenase, subunit D / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Aspartate decarboxylase-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Tungsten formylmethanofuran dehydrogenase, subunit D (FwdD-2)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEletsky, A. / Wu, Y. / Yee, A. / Fares, C. / Lee, H.W. / Arrowsmith, C.H. / Prestegard, J.H. / Szyperski, T. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of tungsten formylmethanofuran dehydrogenase subunit D from Archaeoglobus fulgidus
Authors: Eletsky, A. / Wu, Y. / Yee, A. / Fares, C. / Lee, H.W. / Arrowsmith, C.H. / Prestegard, J.H. / Szyperski, T.
History
DepositionApr 28, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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
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
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tungsten formylmethanofuran dehydrogenase, subunit D (FwdD-2)


Theoretical massNumber of molelcules
Total (without water)16,1691
Polymers16,1691
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 Tungsten formylmethanofuran dehydrogenase, subunit D (FwdD-2)


Mass: 16169.165 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: VC-16 / Gene: AF_1928 / Plasmid: p15Tv lic / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 gold magic / References: UniProt: O28351

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C CT-HSQC aliphatic
1412D 1H-13C CT-HSQC aromatic
1513D HNCO
1613D HN(CA)CO
1713D CBCA(CO)NH
1813D HN(CA)CB
1913D HBHA(CO)NH
1101(4,3)D GFT (H)CCH-COSY aliphatic
11113D (H)CCH-TOCSY aliphatic
1121(4,3)D GFT (H)CCH-COSY aromatic
11313D 1H-15N,13C NOESY
11413D 1H-13C NOESY
11512D MEXICO
11612D CLEANEX
11722D 1H-13C CT-HSQC methyl
11822D 1H-15N HSQC
11922D 1H-15N TROSY
22032D 1H-15N HSQC
22132D 1H-15N TROSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-100% 13C; U-100% 15N] AtT7 protein, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [U-7% 13C; U-100% 15N] AtT7 protein, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 90% H2O/10% D2O90% H2O/10% D2O
30.4 mM [U-7% 13C; U-100% 15N] AtT7 protein, 6.6 mM TRIS, 200 mM sodium chloride, 0.7 mM benzamidine, 13.25 g/L Pf1 phage, 86% H2O/14% D2O86% H2O/14% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMAtT7 protein[U-100% 13C; U-100% 15N]1
10 mMTRIS1
300 mMsodium chloride1
1 mMbenzamidine1
0.6 mMAtT7 protein[U-7% 13C; U-100% 15N]2
10 mMTRIS2
300 mMsodium chloride2
1 mMbenzamidine2
0.4 mMAtT7 protein[U-7% 13C; U-100% 15N]3
6.6 mMTRIS3
200 mMsodium chloride3
0.7 mMbenzamidine3
13.25 g/LPf1 phage3
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1300 7.0 ambient 298 K
2200 7.0 ambient 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002
Bruker AvanceBrukerAVANCE8003

-
Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.1BVariancollection
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
PROSA6.0.2Guntertprocessing
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
CARA1.8.4Keller and Wuthrichchemical shift assignment
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CSI2Wishart and Sykesdata analysis
TALOS2007.068.09.07Shen, Cornilescu, Delaglio and Baxdata analysis
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructure2.1.1Huang, Tejero, Powers and Montelionestructure validation
PSVS1.3Bhattacharya and Montelionestructure validation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed iteratively with CYANA v2.1 and CYANA v3.0 using NOE-based constraints, PHI and PSI dihedral angle constraints from TALOS, hydrogen bond constraints ...Details: Structure determination was performed iteratively with CYANA v2.1 and CYANA v3.0 using NOE-based constraints, PHI and PSI dihedral angle constraints from TALOS, hydrogen bond constraints based on preliminary structures and CLEANEX/MEXICO data, and RDCs from a single alignment medium. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field.
NMR constraintsNOE constraints total: 2670 / NOE intraresidue total count: 633 / NOE long range total count: 934 / NOE medium range total count: 427 / NOE sequential total count: 676 / Hydrogen bond constraints total count: 188 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 59 / Protein psi angle constraints total count: 59
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.1 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 2.6 ° / Maximum upper distance constraint violation: 0.43 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