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- PDB-4uet: Diversity in the structures and ligand binding sites among the fa... -

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Basic information

Entry
Database: PDB / ID: 4uet
TitleDiversity in the structures and ligand binding sites among the fatty acid and retinol binding proteins of nematodes revealed by Na-FAR-1 from Necator americanus
ComponentsNEMATODE FATTY ACID RETINOID BINDING PROTEIN
KeywordsRETINOL-BINDING PROTEIN / FATTY ACID BINDING / RETINOL BINDING / ALL-ALPHA
Function / homologyNematode fatty acid retinoid binding / Nematode fatty acid retinoid binding protein (Gp-FAR-1) / lipid binding / extracellular region / Nematode fatty acid retinoid binding protein
Function and homology information
Biological speciesNECATOR AMERICANUS (New World hookworm)
MethodSOLUTION NMR
AuthorsRey-Burusco, M.F. / Ibanez Shimabukuro, M. / Griffiths, K. / Cooper, A. / Kennedy, M.W. / Corsico, B. / Smith, B.O. / Griffiths, K.
Citation
Journal: Biochem.J. / Year: 2015
Title: Diversity in the Structures and Ligand Binding Sites of Nematode Fatty Acid and Retinol Binding Proteins Revealed by Na-Far-1 from Necator Americanus.
Authors: Rey Burusco, M.F. / Ibanez Shimabukuro, M. / Gabrielsen, M. / Franchini, G.R. / Roe, A.J. / Griffiths, K. / Zhan, B. / Cooper, A. / Kennedy, M.W. / Corsico, B. / Smith, B.O.
#1: Journal: Biomol.NMR Assignments / Year: 2014
Title: 1H, 13C and 15N Chemical Shift Assignments of Na-Far-1, a Helix-Rich Fatty Acid and Retinol Binding Protein of the Parasitic Nematode Necator Americanus.
Authors: Rey-Burusco, M.F. / Ibanez-Shimabukuro, M. / Cooper, A. / Kennedy, M.W. / Corsico, B. / Smith, B.O.
History
DepositionDec 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEMATODE FATTY ACID RETINOID BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,8041
Polymers18,8041
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100BEST RESTRAINT ENERGY
Representative

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Components

#1: Protein NEMATODE FATTY ACID RETINOID BINDING PROTEIN / NA-FAR-1


Mass: 18803.533 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-175
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NECATOR AMERICANUS (New World hookworm)
Plasmid: PET11D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: W2SRJ3
Sequence detailsINCLUDES N-TERMINAL NON-CLEAVABLE HIS-TAG AND CLONING ARTEFACT.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111C HSQC3
121C NOESY
131CBCACONH3
141CBHD
151CBHE
161COSY
171HCCHTOCSY3 1
181HNCACB3
191HNCACO3
1101HNCO3
1111HSQC3 5
1121HCCCONH3
1131N NOESY
1141(H)CCH TOCSY3
1151HCCCONH3
1161P A CAHA D
1171P A CAHA U
1181P A NH D
1191P A NH U
NMR detailsText: INPUT

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Sample preparation

DetailsContents: 95% H2O/5% D2O
Sample conditionsIonic strength: 0.07 / pH: 7.2 / Pressure: 1.0 atm / Temperature: 311.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA 2.3/CNS2.1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
ARIA2.3.1structure solution
CcpNmr Analysis2.1structure solution
CcpNmr Analysis2.1structure solution
DANGLE1.1structure solution
CcpNmr Analysis2.4structure solution
CcpNmr Analysis2structure solution
RefinementSoftware ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: BEST RESTRAINT ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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