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- PDB-1zxf: Solution structure of a self-sacrificing resistance protein, CalC... -

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Basic information

Entry
Database: PDB / ID: 1zxf
TitleSolution structure of a self-sacrificing resistance protein, CalC from Micromonospora echinospora
ComponentsCalC
KeywordsTOXIN / Self-Sacrificing Resistance Protein / Structural Genomics / PSI / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homologyActivator of Hsp90 ATPase homolog 1-like protein / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / CalC
Function and homology information
Biological speciesMicromonospora echinospora (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsSingh, S. / Hager, M.H. / Zhang, C. / Griffith, B.R. / Lee, M.S. / Hallenga, K. / Markley, J.L. / Thorson, J.S. / Center for Eukaryotic Structural Genomics (CESG)
Citation
Journal: Acs Chem.Biol. / Year: 2006
Title: Structural insight into the self-sacrifice mechanism of enediyne resistance.
Authors: Singh, S. / Hager, M.H. / Zhang, C. / Griffith, B.R. / Lee, M.S. / Hallenga, K. / Markley, J.L. / Thorson, J.S.
#1: Journal: Science / Year: 2003
Title: Resistance to enediyne antitumor antibiotics by CalC self-sacrifice.
Authors: Biggins, J.B. / Onwueme, K.C. / Thorson, J.S.
#2: Journal: Science / Year: 2002
Title: The calicheamicin gene cluster and its iterative type I enediyne PKS.
Authors: Ahlert, J. / Shepard, E. / Lomovskaya, N. / Zazopoulos, E. / Staffa, A. / Bachmann, B.O. / Huang, K. / Fonstein, L. / Czisny, A. / Whitwam, R.E. / Farnet, C.M. / Thorson, J.S.
History
DepositionJun 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2005Provider: 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: CalC


Theoretical massNumber of molelcules
Total (without water)17,9151
Polymers17,9151
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein CalC


Mass: 17915.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: CalC / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)GOLD / Keywords: AAM70338 / References: UniProt: Q8KNF0

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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
NMR detailsText: NOESY mixing time = 100 ms

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Sample preparation

DetailsContents: 1mM CalC U-15N,13C; 10mM phosphate buffer, 150 mM NaCl, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1150 mM NaCl 7.3Ambient 303 K
2150 mM NaCl 7.3Ambient 293 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 INOVAVarianINOVA9001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2F. Delaglioprocessing
NMRView5.0.4Johnson, B. Adata analysis
CNS1.1A.T.Brungerstructure solution
ARIA1.2Michael Nilgesstructure solution
ARIA1.2Michael Nilgesrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: The structures are based on a total of 3042 restraints, 2766 are NOE-derived distance constraints, 176 dihedral angle restraints,100 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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