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- PDB-2pq4: NMR solution structure of NapD in complex with NapA1-35 signal peptide -

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Basic information

Entry
Database: PDB / ID: 2pq4
TitleNMR solution structure of NapD in complex with NapA1-35 signal peptide
Components
  • Periplasmic nitrate reductase precursor
  • Protein napD
KeywordsCHAPERONE/OXIDOREDUCTASE / NapD/NapA1-35 / MIXED BETA-ALPHA SANDWICH STRUCTURE / PROTEIN-PEPTIDE COMPLEX / ALPHA-HELIX / Structural Genomics / PSI / Protein Structure Initiative / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / CHAPERONE-OXIDOREDUCTASE COMPLEX
Function / homology
Function and homology information


nitrate reductase complex / nitrate reductase (cytochrome) / nitrate reductase (cytochrome) activity / negative regulation of protein transport / nitrate reductase activity / molybdenum ion binding / anaerobic respiration / Mo-molybdopterin cofactor biosynthetic process / signal sequence binding / molybdopterin cofactor binding ...nitrate reductase complex / nitrate reductase (cytochrome) / nitrate reductase (cytochrome) activity / negative regulation of protein transport / nitrate reductase activity / molybdenum ion binding / anaerobic respiration / Mo-molybdopterin cofactor biosynthetic process / signal sequence binding / molybdopterin cofactor binding / nitrate assimilation / outer membrane-bounded periplasmic space / 4 iron, 4 sulfur cluster binding / electron transfer activity / periplasmic space / iron ion binding / cytoplasm
Similarity search - Function
Chaperone NapD, nitrate reductase assembly / NapD protein / Periplasmic nitrate reductase, large subunit / Nitrate reductase NapA-like, molybdopterin-binding domain / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain ...Chaperone NapD, nitrate reductase assembly / NapD protein / Periplasmic nitrate reductase, large subunit / Nitrate reductase NapA-like, molybdopterin-binding domain / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
Chaperone NapD / Periplasmic nitrate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / CYANA2.1 TORSION ANGLE DYNAMICS
AuthorsMinailiuc, O.M. / Ekiel, I. / Milad, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: To be Published
Title: Solution structure of NapD, a private chaperone of periplasmic nitrate reductase NapA/B, in complex with NapA1-35 signal peptide.
Authors: Minailiuc, O.M. / Ekiel, I. / Cheng, J. / Milad, M. / Gandhi, S. / Larocque, R. / Cygler, M. / Matte, A.
History
DepositionMay 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein napD
B: Periplasmic nitrate reductase precursor


Theoretical massNumber of molelcules
Total (without water)13,1892
Polymers13,1892
Non-polymers00
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 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein napD


Mass: 9755.718 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: napD, b2207, JW2195 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A9I5
#2: Protein/peptide Periplasmic nitrate reductase precursor


Mass: 3433.082 Da / Num. of mol.: 1 / Fragment: Signal peptide: Residues 1-35
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: napA, b2206, JW2194 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P33937, nitrate reductase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 15N/13C-FILTERED/EDITED NOESY
1412D 15N/13C-DOUBLE FILTERED NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3 mM NAPD U-15N and/or U-13C, 1.6 mM NAPA1-3550mM Sodium phosphate buffer, 0.15M NaCl, 0.02% NaN3, 0.001M DTT, 0.2mM PMSF, pH 5.9, 10% D2O or 100% D2O
21.0-1.2 mM NAPA1-35 U-15N and/or U-13C, 1.6-2.0 mM NAPD50mM Sodium phosphate buffer, 0.15M NaCl, 0.02% NaN3, 0.001M DTT, 0.2mM PMSF, pH 5.9, 10% D2O or 100% D2O
Sample conditionsIonic strength: 50mM NaHPO4, 0.150M NaCl / pH: 5.9 / Pressure: 1 atm / Temperature: 312.4 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
Bruker AVANCEBrukerAVANCE5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, P.structure solution
CARA/NEASY1.5.5Keller, R.data analysis
XwinNMR3.5Bruker BioSpinprocessing
NMRPipe2.2Delaglio, F., Grzesiek, S., Bax, A.processing
X-PLOR-NIH NMR2.11.2Schwieters, C.D., Kuszewski, J.J., Tjandra, N., Clore, G.M.refinement
RefinementMethod: CYANA2.1 TORSION ANGLE DYNAMICS / Software ordinal: 1
Details: XPLOR-NIH NMR 2112 REFINE algorithm for structure refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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