[English] 日本語
Yorodumi
- PDB-1sx1: Solution NMR Structure and X-ray Absorption Analysis of the C-Ter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sx1
TitleSolution NMR Structure and X-ray Absorption Analysis of the C-Terminal Zinc-Binding Domain of the SecA ATPase
ComponentsSecA
KeywordsPROTEIN TRANSPORT / zinc / metal ion / tetrahedral coordination / no secondary structure / structural zinc coordination
MethodSOLUTION NMR / simulated annealing
AuthorsDempsey, B.R. / Wrona, M. / Moulin, J.M. / Gloor, G.B. / Jalilehvand, F. / Lajoie, G. / Shaw, G.S. / Shilton, B.H.
CitationJournal: Biochemistry / Year: 2004
Title: Solution NMR Structure and X-ray Absorption Analysis of the C-Terminal Zinc-Binding Domain of the SecA ATPase.
Authors: Dempsey, B.R. / Wrona, M. / Moulin, J.M. / Gloor, G.B. / Jalilehvand, F. / Lajoie, G. / Shaw, G.S. / Shilton, B.H.
History
DepositionMar 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / 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 / _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: SecA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,4912
Polymers2,4261
Non-polymers651
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 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

-
Components

#1: Protein/peptide SecA /


Mass: 2425.836 Da / Num. of mol.: 1 / Fragment: C-terminal Zinc Binding Domain / Source method: obtained synthetically
Details: Solid phase peptide synthesis, N-terminally acetylated. The sequence of this peptide naturally exists in ESCHERICHIA COLI.
#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
113DQF-COSY
2222D NOESY
2342D NOESY
NMR detailsText: This structure was determined using standard two-dimensional 1H NMR techniques. This set of structures is the calculation of the final fold of the domain using restraints for zinc coordination ...Text: This structure was determined using standard two-dimensional 1H NMR techniques. This set of structures is the calculation of the final fold of the domain using restraints for zinc coordination based on EXAFS data for this domain. A second set of structures has been deposited that shows the calculation of the initial fold of the ZBD without using zinc restraints. For remark 500: The bond length is specificed by CNS and not a problem with the structure refinement.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.7mM SecA Zinc Binding Domain NA; 20mM deuterated Pipes buffer, 50mM NaCl, 5mM NaN3, 0.5mM TCEP, 3.4mM ZnCl2, 90% H2O, 10% D2O90% H2O/10% D2O
23.5mM SecA Zinc Binding Domain NA; 20mM deuterated Pipes buffer, 50mM NaCl, 5mM NaN3, 0.5mM TCEP, 7mM ZnCl2, 90% H2O, 10% D2O90% H2O/10% D2O
31.7mM SecA Zinc Binding Domain NA; 20mM deuterated Pipes buffer, 50mM NaCl, 5mM NaN3, 0.5mM TCEP, 3.4mM ZnCl2, 100% D2O100% D2O
43.5mM SecA Zinc Binding Domain NA; 20mM deuterated Pipes buffer, 50mM NaCl, 5mM NaN3, 0.5mM TCEP, 7mM ZnCl2, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM NaCl, 5mM NaN3, 3.4mM ZnCl2 7.0 ambient 298 K
250mM NaCl, 5mM NaN3, 7mM ZnCl2 7.0 ambient 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY5001
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger et al.structure solution
NMRPipe2.1Delaglio et al.processing
VNMR6.1cVarianprocessing
Pipp/Stapp4.3.3Garrett et al.data analysis
CNS1.1Brunger et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: structures based on 317 restraints, 274 are NOE-derived distance restraints, 33 are dihedral angle restraints, and 10 are restraints for the tetrahedral coordination of zinc by 3Cys and 1 His.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
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