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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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.
#2: Chemical ChemComp-ZN / ZINC ION


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

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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 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.

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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 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

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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 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

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