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- PDB-1z2q: High-resolution solution structure of the LM5-1 FYVE domain from ... -

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Basic information

Entry
Database: PDB / ID: 1z2q
TitleHigh-resolution solution structure of the LM5-1 FYVE domain from Leishmania major
ComponentsLM5-1
KeywordsMEMBRANE PROTEIN / FYVE domain / Zinc-finger
Function / homologyZinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 2-Layer Sandwich / Alpha Beta
Function and homology information
Biological speciesLeishmania major (eukaryote)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing.
Model type detailsminimized average
AuthorsMertens, H.D.T. / Callaghan, J.M. / McConville, M.J. / Gooley, P.R.
CitationJournal: Protein Sci. / Year: 2007
Title: A high-resolution solution structure of a trypanosomatid FYVE domain.
Authors: Mertens, H.D.T. / Callaghan, J.M. / Swarbrick, J.D. / McConville, M.J. / Gooley, P.R.
History
DepositionMar 8, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LM5-1


Theoretical massNumber of molelcules
Total (without water)9,1691
Polymers9,1691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #21minimized average structure

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Components

#1: Protein LM5-1


Mass: 9169.424 Da / Num. of mol.: 1 / Fragment: FYVE domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Plasmid: pGEX-6P-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA
1423D 13C-separated NOESY
1532D 13C-ct-HSQC
1642D 15N-HSQC-TROSY, 2D HN(a/b-NC-J)-TROSY, 2D HN(CO-a/b-C'CA-J)-TROSY, 3D 1H-dec HN(CO)CA
NMR detailsText: 2 x Zn2+ ions not included in calculations, ligating cysteines treated as protonated sulfhydryl groups during simulated annealing.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM LM5-1 U-15N, 13C; 50mM sodium phosphate buffer, 50mM KCl, 1mM DTT, 1mM AEBSF, 0.05% sodium azide; 90% H2O, 10% D2O90% H2O/10% D2O
20.8mM LM5-1 U-15N,13C; 50mM sodium phosphate buffer, 50mM KCl, 1mM DTT, 1mM AEBSF,0.05% sodium azide; 100% D2O99.99% D2O
30.8mM LM5-1 ~10% 13C; 50mM sodium phosphate buffer, 50mM KCl, 1mM DTT, 1mM AEBSF, 0.05% sodium azide; 100% D2O90% H2O/10% D2O
40.8mM LM5-1 U-15N,13C; 50mM sodium phosphate buffer, 50mM KCl, 1mM DTT, 1mM AEBSF, 0.05% sodium azide; 10mg/ml PF1; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionspH: 7.4 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1cVarian inc.collection
NMRPipe2.2Delaglioprocessing
XEASY1.3Bartelsdata analysis
CYANA1.0.7Guntertstructure solution
Xplor-NIH2.9.1refinement
RefinementMethod: torsion angle dynamics, simulated annealing. / Software ordinal: 1
Details: Structures based on 545 NOE-derived distance constraints, 101 dihedral angle restraints, and 259 residual dipolar couplings.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 21

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