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- PDB-1fh1: BACKBONE FOLD OF NODF -

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Basic information

Entry
Database: PDB / ID: 1fh1
TitleBACKBONE FOLD OF NODF
ComponentsNODULATION PROTEIN F
KeywordsLIPID BINDING PROTEIN / ROOT NODULATION FACTOR / PROTEIN BACKBONE FOLD
Function / homologynodulation / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Nodulation protein F
Function and homology information
Biological speciesRhizobium leguminosarum (bacteria)
MethodSOLUTION NMR / other
AuthorsFowler, C.A. / Tian, F. / Al-Hashimi, H.M. / Prestegard, J.H.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Rapid determination of protein folds using residual dipolar couplings.
Authors: Fowler, C.A. / Tian, F. / Al-Hashimi, H.M. / Prestegard, J.H.
#1: Journal: FEBS Lett. / Year: 1996
Title: NMR Investigations of the Structural Properties of the Nodulation Protein, NodF, from Rhizobium Leguminosarum and its Homology with Eschericia Coli Acyl Carrier Protein
Authors: Ghose, R. / Geiger, O. / Prestegard, J.H.
History
DepositionJul 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: NODULATION PROTEIN F


Theoretical massNumber of molelcules
Total (without water)9,9511
Polymers9,9511
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)1 / -
Representative

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Components

#1: Protein NODULATION PROTEIN F / NODF


Mass: 9951.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium leguminosarum (bacteria) / Plasmid: PMP2301 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04685

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: Assignments were made using double and triple-resonance NMR spectroscopy. Dipolar couplings were measured and used to produce the protein backbone fold.

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Sample preparation

Details
Solution-IDContentsSolvent system
12.5 mM NodF isotropic U-15N,13C 200 mM phosphate buffer, pH 6.190% H2O/10% D2O
21.0 mM NodF aligned U-15N,13C 200 mM phosphate buffer, pH 6.1 20 mg/mL Pf1 bacteriophage90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 6.1 ambient 298 K
20 6.1 ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
Felix98MSIprocessing
Orderten_SVDLosonczidata analysis
POSEFowlerstructure solution
POSEFowlerrefinement
RefinementMethod: other / Software ordinal: 1
Details: secondary structural elements (3 helices) were identified. these were split into smaller fragments and individual fragments were oriented using residual dipolar coupling data and the program ...Details: secondary structural elements (3 helices) were identified. these were split into smaller fragments and individual fragments were oriented using residual dipolar coupling data and the program Orderten_SVD (Losonczi, et al., J. Magn. Res., 138, 334-342, 1999). The fragments were reassembled and then positioned spatially by translation using a limited set of NOEs to produce a backbone fold of the nodF protein. THERE ARE N-CA-C ANGLE ERRORS (AS COMPARED TO THE STANDARD DICTIONARY) AT RESIDUES 13 AND 80. RESIDUE 80 LIES SOMEWHAT OUTSIDE ALLOWED RAMACHANDRAN SPACE. THESE SITES ARE POSITIONS WHERE ORIENTED HELICAL FRAGMENTS WERE REASSEMBLED INTO COMPLETE HELICES DURING DETERMINATION OF OF THE BACKBONE FOLD AND ANY SMALLER LOCAL DISTORTIONS FROM IDEALITY ARE EXPECTED TO CONCENTRATE HERE. THE STRUCTURE PRESENTED HERE CONTAINS ONLY COORDINATES FOR BACKBONE ATOMS INVOLVED IN SECONDARY STRUCTURE. THE STRUCTURE IS THE AVERAGE OF AN ENSEMBLE WITH A HEAVY ATOM RMSD OF 2.4 ANGSTROMS. CB POSITIONS COME FROM POLYALANINE HELICES USED TO MODEL THE BACKBONE.
NMR ensembleConformers submitted total number: 1

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