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- PDB-2def: PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 20 STRU... -

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Basic information

Entry
Database: PDB / ID: 2def
TitlePEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 20 STRUCTURES
ComponentsPEPTIDE DEFORMYLASE
KeywordsHYDROLASE / METALLOPROTEASE
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
NICKEL (II) ION / Peptide deformylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / DISTANCE GEOMETRY, RESTRAINED SIMULATED ANNEALING
AuthorsMeinnel, T. / Dardel, F.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Solution structure of nickel-peptide deformylase.
Authors: Dardel, F. / Ragusa, S. / Lazennec, C. / Blanquet, S. / Meinnel, T.
#1: Journal: FEBS Lett. / Year: 1996
Title: The C-Terminal Domain of Peptide Deformylase is Disordered and Dispensable for Activity
Authors: Meinnel, T. / Lazennec, C. / Dardel, F. / Schmitter, J.M. / Blanquet, S.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: A New Subclass of the Zinc Metalloproteases Superfamily Revealed by the Solution Structure of Peptide Deformylase
Authors: Meinnel, T. / Blanquet, S. / Dardel, F.
#3: Journal: J.Mol.Biol. / Year: 1995
Title: Mapping of the Active Site Zinc Ligands of Peptide Deformylase
Authors: Meinnel, T. / Lazennec, C. / Blanquet, S.
#4: Journal: J.Bacteriol. / Year: 1993
Title: Evidence that Peptide Deformylase and Methionyl-tRNA(Fmet) Formyltransferase are Encoded within the Same Operon in Escherichia Coli
Authors: Meinnel, T. / Blanquet, S.
History
DepositionDec 15, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: PEPTIDE DEFORMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7042
Polymers16,6451
Non-polymers591
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 / 200LOWEST DIANA TARGET FUNCTION
Representative

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Components

#1: Protein PEPTIDE DEFORMYLASE


Mass: 16645.125 Da / Num. of mol.: 1 / Fragment: ACTIVE CATALYTIC CORE, RESIDUES 1 - 147 / Mutation: S1A
Source method: isolated from a genetically manipulated source
Details: ACTIVE FORM CONTAINING ONE NICKEL ION IN THE METAL BINDING SITE
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PAL421TR / Gene: FMS (CODONS 1-147) / Plasmid: PUC18 (IPTG-INDUCIBLE LAC PROMOTOR), PDEF-EC1-147 / Gene (production host): FMS (CODONS 1-147) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6K3, EC: 3.5.1.31
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131CT-HSQC
141HNCA
151NOESY-HMQC
161(H)CCH-TOCSY
171HMBC-HSQC
181HNHB

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Sample preparation

Sample conditionspH: 7.2 / Temperature: 318 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 & DRX600 / Manufacturer: Bruker / Model: AMX600 & DRX600 / Field strength: 600 MHz

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameVersionDeveloperClassification
X-PLORBRUNGERrefinement
DIANA, X-PLOR3.1X-PLOR3.1structure solution
RefinementMethod: DISTANCE GEOMETRY, RESTRAINED SIMULATED ANNEALING / Software ordinal: 1
Details: RESTRAINED SIMULATED ANNEALING USING 1948 NOE RESTRAINTS -389 INTRARESIDUE -330 SEQUENTIAL -328 MEDIUM RANGE -901 LONG RANGE 227 DIHEDRAL ANGLE RESTRAINTS -96 PHI -13 PSI -118 CHI1 86 RESTRAINTS FOR 43 H-BONDS
NMR ensembleConformer selection criteria: LOWEST DIANA TARGET FUNCTION / Conformers calculated total number: 200 / Conformers submitted total number: 20

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