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- PDB-1def: PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 9 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1def
TitlePEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 9 STRUCTURES
ComponentsPEPTIDE DEFORMYLASE
KeywordsHYDROLASE / ZINC METALLOPROTEASE
Function / homology
Function and homology information


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
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR
AuthorsMeinnel, T. / Dardel, F.
Citation
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.
#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: 1995
Title: Mapping of the Active Site Zinc Ligands of Peptide Deformylase
Authors: Meinnel, T. / Lazennec, C. / Blanquet, S.
#3: 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
DepositionMar 19, 1996Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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)16,7272
Polymers16,6611
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)9 / -
Representative

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Components

#1: Protein PEPTIDE DEFORMYLASE


Mass: 16661.125 Da / Num. of mol.: 1 / Fragment: ACTIVE CATALYTIC CORE, RESIDUES 1 - 147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PAL421TR / Description: PUC18 (IPTG-INDUCIBLE LAC PROMOTER) / Gene: FMS (CODONS 1-147) / Plasmid: 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: IN 20 MM POTASSIUM PHOSPHATE

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Sample preparation

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

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 9

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