[English] 日本語
Yorodumi
- PDB-2azh: Solution structure of iron-sulfur cluster assembly protein SUFU f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2azh
TitleSolution structure of iron-sulfur cluster assembly protein SUFU from Bacillus subtilis, with zinc bound at the active site. Northeast Structural Genomics Consortium target SR17
ComponentsSufU
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SR17 / autostructure / iron-sulfur / zinc / ISCU / SUFU / NIFU-like / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Transferases / iron-sulfur cluster assembly / ferrous iron binding / 2 iron, 2 sulfur cluster binding / transferase activity / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Sufe protein. Chain: A - #10 / Sufe protein. Chain: A / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Zinc-dependent sulfurtransferase SufU
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / MINIMAL CONSTRAINT STRUCTURE, CONTAINED 512 CONFORMATIONALLY RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 54 HYDROGEN BONDED PAIRS, 186 RESIDUAL DIPOLAR COUPLING CONSTRAINTS, 197 DIHEDRAL ANGLE CONSTRAINTS. 7.0 CONSTRAINTS PER CONFORMATIONALLY CONSTRAINED RESIDUE. 1.0 LONG RANGE CONSTRAINT PER RESIDUE.
AuthorsKornhaber, G.J. / Swapna, G.V.T. / Ramelot, T.A. / Cort, J.R. / Aramini, J.M. / Kennedy, M.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be published
Title: Solution NMR Structure of Zn-Ligated Fe-S Cluster Assembly Scaffold Protein SufU From Bacillus subtilis
Authors: Kornhaber, G.J. / Swapna, G.V.T. / Ramelot, T.A. / Cort, J.R. / Aramini, J.M. / Kennedy, M.A. / Montelione, G.T.
History
DepositionSep 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: 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_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SufU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2512
Polymers16,1851
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 60structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein SufU / IscU


Mass: 16185.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YURV / Plasmid: PET21D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMGK / References: UniProt: O32163
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 15N-1H HSQC, 2D 13C-1H HSQC, 3D HNCO, 3D HNCA, 3D HN(CO)CA, 3D HN(CA)CB, 3D HN(CO)CACB, 3D (H)CC(CO)NH-TOCSY, 3D (H)CC(CO)NH-TOCSY
2222D HH NOESY, 2D 13C-1H HSQC, 2D 15N-1H HSQC, 3D 15N-NOESY, 3D 13C-NOESY, 4D CC NOESY
2332D 13C-1H HSQC
1442D 15N-1H IPAP-HSQC
1552D 15N-1H IPAP-HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.7 MM U-15N, U-13C, PERDEUTERATEDSUFU WITH 13C,1H-LEU, VAL AND ILE-DELTA METHYLS, IN 50MM SODIUM PHOSPHATE, 100MM NACL, 1MM DTT, 0.02% NAN3, 5% D2O, 95% H2O5% D2O, 95% H2O
21.0 MM U-15N, U-13C, PERDEUTERATED SUFU WITH 13C,1H-LEU, VAL AND ILE-DELTA METHYLS AND 12C,15N,1H - PHE,TYR IN 100MM POTASSIUM PHOSPHATE, 200MM GLYCEROL, 1MM DTT, 0.02% NAN3, 5% D2O, 95% H2O5% D2O, 95% H2O
31.0 MM U-5%13C, U-15N SUFU IN 100MM POTASSIUM PHOSPHATE, 200MM GLYCEROL, 1MM DTT, 0.02% NAN3, 5% D2O, 95% H2O5% D2O, 95% H2O
40.8 mM U-5%13C, U-15N SUFU IN 50MM SODIUM PHOSPHATE, 100MM NACL, 1MM DTT, 0.02% NAN3, 5% HEXAETHYLENE GLYCOL MONODODECYL ETHER/N-HEXANOL, 90% H2O, 5% D2O90% H2O, 5% D2O
50.8 mM U-5%13C, U-15N SUFU IN 50MM SODIUM PHOSPHATE, 100MM NACL, 1MM DTT, 0.02% NAN3, 3.5% PENTAETHYLENE GLYCOL ETHER/N-OCTANOL, 91.5% H2O, 5% D2O91.5% H2O, 5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mM NaCl, 50mM Sodium Phosphate 6.5 ambient 20 K
2100mM Potassium Phosphate 6.5 ambient 20 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503
Varian INOVAVarianINOVA8004

-
Processing

NMR software
NameVersionDeveloperClassification
AUTOSTRUCTURE-DYANA1.1.2Huang, Montelione et al.structure solution
XPLOR-NIH2.0.6Schwieters, Clore et al.structure solution
TALOS2.1Cornilescu, Bax et al.data analysis
NMRPipe2.1Delaglio, Bax et al.processing
AutoAssign1.9Zimmerman, Montelione et al.data analysis
Sparky3.2Goddard, Kneller et al.data analysis
PdbStat3.2Tejero, Montelione et al.data analysis
PALES2.1Zweckstetterdata analysis
XPLOR-NIH2.0.6refinement
RefinementMethod: MINIMAL CONSTRAINT STRUCTURE, CONTAINED 512 CONFORMATIONALLY RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 54 HYDROGEN BONDED PAIRS, 186 RESIDUAL DIPOLAR COUPLING CONSTRAINTS, 197 DIHEDRAL ...Method: MINIMAL CONSTRAINT STRUCTURE, CONTAINED 512 CONFORMATIONALLY RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 54 HYDROGEN BONDED PAIRS, 186 RESIDUAL DIPOLAR COUPLING CONSTRAINTS, 197 DIHEDRAL ANGLE CONSTRAINTS. 7.0 CONSTRAINTS PER CONFORMATIONALLY CONSTRAINED RESIDUE. 1.0 LONG RANGE CONSTRAINT PER RESIDUE.
Software ordinal: 1
Details: DETERMINATION WAS PERFORMED WITH THE FOLLOWING STEPS: RESONANCE ASSIGNMENTS, TORTION ANGLE CONTRAINTS, HYDROGEN BONDED PAIRS AND NOESY CROSSPEAK DATA WAS USED AS INPUT INTO AUTOSTRUCTURE- ...Details: DETERMINATION WAS PERFORMED WITH THE FOLLOWING STEPS: RESONANCE ASSIGNMENTS, TORTION ANGLE CONTRAINTS, HYDROGEN BONDED PAIRS AND NOESY CROSSPEAK DATA WAS USED AS INPUT INTO AUTOSTRUCTURE-DYANA. AUTOSTRUCTURE-DYANA IDENTIFIED DISTANCE CONSTRAINTS. THESE DISTANCE CONSTRAINTS WERE USED AS INPUT INTO AN XPLOR-NIH SIMULATED ANNEALING. USING CNS THE TOP TEN XPLOR-NIH STRUCTURES WERE ENERGY MINIMIZED IN EXPLICIT WATER WITH RDC CONSTRAINTS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 10

+
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://pdbjlvh1.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