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Basic information

Entry
Database: PDB / ID: 1sx0
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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SecA


Theoretical massNumber of molelcules
Total (without water)2,4261
Polymers2,4261
Non-polymers00
Water00
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

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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

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Experimental details

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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 initial fold of the domain without using restraints for zinc ...Text: This structure was determined using standard two-dimensional 1H NMR techniques. This set of structures is the calculation of the initial fold of the domain without using restraints for zinc coordination. A second set of structures has been deposited that is a refinement of this fold using zinc coordination restraints based on EXAFS data for this domain.

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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 ZnCl290% H2O/10% D2O
23.5mM SecA Zinc Binding Domain NA; 20mM deuterated Pipes buffer, 50mM NaCl, 5mM NaN3, 0.5mM TCEP, 7mM ZnCl290% H2O/10% D2O
31.7mM SecA Zinc Binding Domain NA; 20mM deuterated Pipes buffer, 50mM NaCl, 5mM NaN3, 0.5mM TCEP, 3.4mM ZnCl2100% D2O
43.5mM SecA Zinc Binding Domain NA; 20mM deuterated Pipes buffer, 50mM NaCl, 5mM NaN3, 0.5mM TCEP, 7mM ZnCl2100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM NaCl, 5mM NaN3, 3.4mM ZnCl2 7ambient 298 K
250mM NaCl, 5mM NaN3, 7mM ZnCl2 7ambient 298 K

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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

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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 307 restraints, 274 are NOE-derived distance restraints, 33 are dihedral angle restraints.
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

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