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- PDB-2kmn: Solution structure of peptide deformylase complexed with actinonin -

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Basic information

Entry
Database: PDB / ID: 2kmn
TitleSolution structure of peptide deformylase complexed with actinonin
ComponentsPeptide deformylase
KeywordsHYDROLASE/ANTIBIOTIC / Peptide Deformylase / Actinonin / Hydrolase / Iron / Metal-binding / Protein biosynthesis / HYDROLASE-ANTIBIOTIC COMPLEX
Function / homology
Function and homology information


co-translational protein modification / peptide deformylase / peptide deformylase activity / ferrous iron binding / ribosome binding / hydrolase activity / translation / zinc ion binding / cytosol
Similarity search - Function
Peptide Deformylase / Peptide deformylase / Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACTINONIN / Peptide deformylase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMcElroy, C.A. / Amero, C.D. / Byerly, D.W. / Foster, M.P.
Citation
Journal: To be Published
Title: Solution Structure of Peptide Deformylase complexed with Actinonin
Authors: McElroy, C.A. / Amero, C.D. / Byerly, D.W. / Foster, M.P.
#1: Journal: Biochemistry / Year: 2009
Title: Ligand-induced changes in the structure and dynamics of Escherichia coli peptide deformylase.
Authors: Amero, C.D. / Byerly, D.W. / McElroy, C.A. / Simmons, A. / Foster, M.P.
History
DepositionAug 1, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 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: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1123
Polymers16,6611
Non-polymers4512
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 Peptide deformylase / PDF / Polypeptide deformylase


Mass: 16661.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: def, fms, b3287, JW3248 / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6K3, peptide deformylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BB2 / ACTINONIN / 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2-HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL-PROPYL]-AMIDE


Mass: 385.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H35N3O5 / Comment: antitumor, antibiotic*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution Structure of Peptide Deformylase complexed with Actinonin
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D (H)CCH-TOCSY
1813D (H)CCH-COSY
1913D 1H-15N TOCSY
11013D 1H-15N NOESY
11113D HNHA
11213D HNHB
11313D C(CO)NH

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Sample preparation

DetailsContents: 0.6-1.0 mM [U-100% 13C; U-100% 15N] Protein-1, 1.2 mM ACTINONIN-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMProtein-1[U-100% 13C; U-100% 15N]0.6-1.01
1.2 mMACTINONIN-21
Sample conditionsIonic strength: 10 / pH: 7.2 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX8002
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
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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