[English] 日本語
Yorodumi
- PDB-2k5p: NMR Solution Structure of a Thiamine Biosynthesis Protein from Ge... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2k5p
TitleNMR Solution Structure of a Thiamine Biosynthesis Protein from Geobacter Metallireducens: Northeast Structural Genomics Consortium Target GmR137
Componentsthiamine-biosynthesis protein
KeywordsBIOSYNTHETIC PROTEIN / NESG / GmR137 / Geobacter metallireducens / Thiamine Biosynthesis / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


ThiS, thiamine-biosynthesis / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Thiamin biosynthesis sulfur carrier protein
Similarity search - Component
Biological speciesGeobacter metallireducens GS-15 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsCASP target
AuthorsMani, R. / Wang, H. / Jiang, M. / Magliaqui, M. / Xiao, R. / Nair, R. / Baran, M.C. / Gurla, S.V.T. / Acton, T.B. / Rost, B. ...Mani, R. / Wang, H. / Jiang, M. / Magliaqui, M. / Xiao, R. / Nair, R. / Baran, M.C. / Gurla, S.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR Solution Structure of a Thiamine Biosynthesis Protein from Geobacter Metallireducens: Northeast Structural Genomics Consortium Target GmR137
Authors: Mani, R. / Wang, H. / Jiang, M. / Magliaqui, M. / Xiao, R. / Nair, R. / Baran, M.C. / Gurla, S.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T.
History
DepositionJun 30, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 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 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: thiamine-biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)8,5301
Polymers8,5301
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 / 140structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein thiamine-biosynthesis protein / ThiS protein


Mass: 8530.462 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens GS-15 (bacteria)
Species: metallireducens / Gene: Gmet_1567 / Plasmid: pET 21-23C / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q39VC5

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR / Details: CASP target
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
131(4,3)D GFT-HNNCABCA
141(4,3)D GFT-CABCA(CO)NHN
151(4,3)D GFT-HABCAB(CO)NHN
1613D CBCA(CO)NH
1713D HBHA(CO)NH
1813D HNCO
1913D (H)CCH-TOCSY
11013D-CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C aliph NOESY
11313D 1H-13C arom NOESY
11413D (H)CCH-COSY
21522D 1H-15N HSQC
11612D 1H-15N HSQC
11712D 1H-13C HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.06 mM [U-100% 13C; U-100% 15N] GmR137, THiS protein, 90% H2O/10% D2O90% H2O/10% D2O
21.26 mM [U-10% 13C; U-99% 15N] GmR137, THiS protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.06 mMGmR137, THiS protein[U-100% 13C; U-100% 15N]1
1.26 mMGmR137, THiS protein[U-10% 13C; U-99% 15N]2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
15 mM CaCl2, 100mM NaCl 6.5ambient 293 K
25 mM CaCl2, 100mM NaCl 6.5ambient 293 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003

-
Processing

NMR software
NameVersionDeveloperClassification
CNS2.0.6Brunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AutoAssign2.4.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structure was obtained using triple resonance NMR spectroscopy. GFT-NMR experiments were used for backbone resonance assignments and conventional 3D TOCSY and COSY experiments were used ...Details: The structure was obtained using triple resonance NMR spectroscopy. GFT-NMR experiments were used for backbone resonance assignments and conventional 3D TOCSY and COSY experiments were used to obtain sidechain resonance assignments. Automated NOESY assignments were made using AUTOSTRUCTURE and CYANA-2.1. Dihedral angle constraints were obtained from TALOS. The structure calculation was done excluding 5 HIS from 8-residue C-terminal tag (LEHHHHHH). Completeness of assignments excluding 5-HIS: Backbone - 100%, Sidechain (aliphatic) - 99% Sidechain (aromatic) - 96%. The assignments were validated using AVS software. Final structure quality factros (excluding 5 HIS) determined using PSVS-v1.3: Ordered residues are defiend as: 1-13, 18-29, 32-63. (a) RMSD (ordered residues) all backbone atoms: 0.7A and heavy atoms: 1.2A. (b) Ramachandran statistics for ordered residues: Most favored region: 82.8%, additionally allowed regions: 17.0% generously allowed region: 0.1%, disallowed regions: 0.1%. (c) Procheck scores for ordered residues (RAW/Z-): Phi/psi -0.58/-1.97, all -0.48/-2.84, (d) MolProbity clashscores (RAW/Z-) 17.03/-1.40, (e) RPF scores for the goodness of the fit to NOESY data: Recall - 0.99, Precision - 0.942, F-measure - 0.966 and final dp score - 0.88. (f) Number of close contacts for 20 models: 6, RMS deviation for bond angles - 0.6deg, RMS deviation for bond lengths - 0.009A.
NMR constraintsNOE constraints total: 969 / NOE intraresidue total count: 144 / NOE long range total count: 269 / NOE medium range total count: 207 / NOE sequential total count: 349 / Protein phi angle constraints total count: 41 / Protein psi angle constraints total count: 41
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 140 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.2 Å / Torsion angle constraint violation method: PSVS software
NMR ensemble rmsDistance rms dev: 0.01 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