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- PDB-1tm6: NMR Structure of the Free Zinc Binding C-terminal Domain of SecA -

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Basic information

Entry
Database: PDB / ID: 1tm6
TitleNMR Structure of the Free Zinc Binding C-terminal Domain of SecA
ComponentsPreprotein translocase secA subunit
KeywordsPROTEIN TRANSPORT / Zinc finger / beta hairpin / SecA
Function / homology
Function and homology information


preprotein binding / cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein targeting to membrane / protein secretion / protein targeting ...preprotein binding / cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein targeting to membrane / protein secretion / protein targeting / ribonucleoprotein complex binding / chaperone-mediated protein folding / cytoplasmic side of plasma membrane / ribosome binding / protein transport / zinc ion binding / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
SecA P-loop domain / SEC-C motif / SEC-C motif / SecA, C-terminal helicase domain / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain / SecA motor DEAD / SecA conserved site ...SecA P-loop domain / SEC-C motif / SEC-C motif / SecA, C-terminal helicase domain / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain / SecA motor DEAD / SecA conserved site / SecA, Wing/Scaffold superfamily / SecA, preprotein cross-linking domain superfamily / SecA preprotein cross-linking domain / SecA Wing and Scaffold domain / SecA DEAD-like domain / SecA family signature. / SecA family profile. / SecA DEAD-like domain / SecA preprotein cross-linking domain / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein translocase subunit SecA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / standard x-plor protocol; 1. distance geometry sub-embed 2. distance geometry full embed 3. simulated annealing 4. simulated annealing refine
AuthorsMatousek, W.M. / Alexandrescu, A.T.
CitationJournal: Biochim.Biophys.Acta / Year: 2004
Title: NMR structure of the C-terminal domain of SecA in the free state
Authors: Matousek, W.M. / Alexandrescu, A.T.
History
DepositionJun 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 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: 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.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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_ins_code / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Preprotein translocase secA subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,5042
Polymers2,4391
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 / 500structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function
RepresentativeModel #1closest to the average,fewest violations,lowest energy

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Components

#1: Protein/peptide Preprotein translocase secA subunit


Mass: 2438.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P10408
#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
1112D TOCSY
1212D NOESY
231Natural Abundance N-HSQC
443Natural Abundance C-HSQC
352Hydrogen Exchange
4632D NOESY
473E-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
12.5mM protein, 2.7mM ZnCl, 10mM PO4 buffer10% D2O; 90% H2O
21.4mM protein, 1.6mM ZnCl, 10mM PO4 buffer99.96% D2O
32.5mM protein, 2.7mM ZnCl, 10mM PO4 buffer99% D20; 1% H20
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
12.7mM ZnCl; 10mM PO4 buffer 7.40 1 atm298 K
22.7mM ZnCl; 10mM PO4 buffer 6.03 1 atm298 K
31.6mM ZnCl; 10mM PO4 buffer 6.14 1 atm298 K
42.7mM ZnCl; 10mM PO4 buffer 6.43 1 atm298 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 INOVAVarianINOVA5001
Varian INOVAVarianINOVA5002
Varian INOVAVarianINOVA5003
Varian INOVAVarianINOVA5004

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Processing

NMR software
NameVersionClassification
Felix2000data analysis
X-PLOR3.851refinement
RefinementMethod: standard x-plor protocol; 1. distance geometry sub-embed 2. distance geometry full embed 3. simulated annealing 4. simulated annealing refine
Software ordinal: 1
NMR representativeSelection criteria: closest to the average,fewest violations,lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function
Conformers calculated total number: 500 / Conformers submitted total number: 20

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