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6iy7

E. coli peptide deformylase crystal structure fitted into the cryo-EM density map of E. coli 70S ribosome in complex with peptide deformylase

Method: ELECTRON MICROSCOPY Dmax: 55.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Peptide deformylase

Escherichia coli K-12

UniProt P0A6K3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain P； UniProt 1–169 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 10.50 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6IY7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BS4 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL Deposited 1998-09-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–168（168 aa）
Not recorded ZN ZINC ION × 1 2PE NONAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；REFERENCE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER ( 1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
Resolution 1.90 Å R-free 0.240
1BS4 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL Deposited 1998-09-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–168（168 aa）
Not recorded ZN ZINC ION × 1 2PE NONAETHYLENE GLYCOL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；REFERENCE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER ( 1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
Resolution 1.90 Å R-free 0.240
1BS4 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL Deposited 1998-09-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–168（168 aa）
Not recorded ZN ZINC ION × 1 2PE NONAETHYLENE GLYCOL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；REFERENCE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER ( 1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
Resolution 1.90 Å R-free 0.240
1BS5 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM Deposited 1998-09-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–168（168 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
Resolution 2.50 Å R-free 0.258
1BS5 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM Deposited 1998-09-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–168（168 aa）
Not recorded ZN ZINC ION × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
Resolution 2.50 Å R-free 0.258
1BS5 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM Deposited 1998-09-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–168（168 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
Resolution 2.50 Å R-free 0.258
1BS6 PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER Deposited 1998-09-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–168（168 aa）
Not recorded NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
Resolution 2.10 Å R-free 0.258
1BS6 PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER Deposited 1998-09-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–168（168 aa）
Not recorded NI NICKEL (II) ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
Resolution 2.10 Å R-free 0.258
1BS6 PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER Deposited 1998-09-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–168（168 aa）
Not recorded NI NICKEL (II) ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
Resolution 2.10 Å R-free 0.258
1BS7 PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM Deposited 1998-09-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–168（168 aa）
Not recorded NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
Resolution 2.50 Å R-free 0.272
1BS7 PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM Deposited 1998-09-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–168（168 aa）
Not recorded NI NICKEL (II) ION × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
Resolution 2.50 Å R-free 0.272
1BS7 PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM Deposited 1998-09-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–168（168 aa）
Not recorded NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
Resolution 2.50 Å R-free 0.272
1BS8 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER Deposited 1998-09-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–168（168 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
Resolution 2.20 Å R-free 0.261
1BS8 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER Deposited 1998-09-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–168（168 aa）
Not recorded ZN ZINC ION × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
Resolution 2.20 Å R-free 0.261
1BS8 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER Deposited 1998-09-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–168（168 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
Resolution 2.20 Å R-free 0.261
1BSJ COBALT DEFORMYLASE INHIBITOR COMPLEX FROM E.COLI Deposited 1998-08-28 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–169（168 aa）
Not recorded CO COBALT (II) ION × 1 PO4 PHOSPHATE ION × 1 MLN (S)-2-(PHOSPHONOXY)CAPROYL-L-LEUCYL-P-NITROANILIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 3.00 Å R-free 0.207
1BSK ZINC DEFORMYLASE INHIBITOR COMPLEX FROM E.COLI Deposited 1998-08-28 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–169（168 aa）
Not recorded ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 MLN (S)-2-(PHOSPHONOXY)CAPROYL-L-LEUCYL-P-NITROANILIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 3.00 Å R-free 0.221
1BSZ PEPTIDE DEFORMYLASE AS FE2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL Deposited 1998-09-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–168（168 aa）
Not recorded FE FE (III) ION × 1 2PE NONAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
Resolution 1.90 Å R-free 0.247
1BSZ PEPTIDE DEFORMYLASE AS FE2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL Deposited 1998-09-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–168（168 aa）
Not recorded FE FE (III) ION × 1 2PE NONAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
Resolution 1.90 Å R-free 0.247
1BSZ PEPTIDE DEFORMYLASE AS FE2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL Deposited 1998-09-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–168（168 aa）
Not recorded FE FE (III) ION × 1 2PE NONAETHYLENE GLYCOL × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
Resolution 1.90 Å R-free 0.247
1DEF PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 9 STRUCTURES Deposited 1996-03-19 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–147（147 aa） Fragment：ACTIVE CATALYTIC CORE, RESIDUES 1 - 147
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 7.2；318 K
Resolution not provided
1DFF PEPTIDE DEFORMYLASE Deposited 1997-08-19 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–164（164 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.88 Å R-free 0.289
1G27 CRYSTAL STRUCTURE OF E.COLI POLYPEPTIDE DEFORMYLASE COMPLEXED WITH THE INHIBITOR BB-3497 Deposited 2000-10-17 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–168（168 aa）
Not recorded NI NICKEL (II) ION × 1 BB1 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEXANOIC ACID (1-DIMETHYLCARBAMOYL-2,2-DIMETHYL-PROPYL)-AMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；290 K；10mg/ml PDF, 20mM BB-3497, 25% PEG 4000, 0.1M sodium citrate, 0.2M ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP at 290K
Resolution 2.10 Å R-free 0.270
1G27 CRYSTAL STRUCTURE OF E.COLI POLYPEPTIDE DEFORMYLASE COMPLEXED WITH THE INHIBITOR BB-3497 Deposited 2000-10-17 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–168（168 aa）
Not recorded NI NICKEL (II) ION × 1 BB1 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEXANOIC ACID (1-DIMETHYLCARBAMOYL-2,2-DIMETHYL-PROPYL)-AMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；290 K；10mg/ml PDF, 20mM BB-3497, 25% PEG 4000, 0.1M sodium citrate, 0.2M ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP at 290K
Resolution 2.10 Å R-free 0.270
1G27 CRYSTAL STRUCTURE OF E.COLI POLYPEPTIDE DEFORMYLASE COMPLEXED WITH THE INHIBITOR BB-3497 Deposited 2000-10-17 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–168（168 aa）
Not recorded NI NICKEL (II) ION × 1 BB1 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEXANOIC ACID (1-DIMETHYLCARBAMOYL-2,2-DIMETHYL-PROPYL)-AMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；290 K；10mg/ml PDF, 20mM BB-3497, 25% PEG 4000, 0.1M sodium citrate, 0.2M ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP at 290K
Resolution 2.10 Å R-free 0.270
1G2A THE CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE COMPLEXED WITH ACTINONIN Deposited 2000-10-18 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–168（168 aa）
Not recorded NI NICKEL (II) ION × 1 BB2 ACTINONIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；10mg/ml PDF, 20mM actinonin, 50mM HEPES, pH 7.5 + 25-32% PEG 4000, 0.1M sodium citrate, pH 5.6, 0.2M ammonium acetate, VAPOR DIFFUSION, HANGING DROP at 290K
Resolution 1.75 Å R-free 0.250
1G2A THE CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE COMPLEXED WITH ACTINONIN Deposited 2000-10-18 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–168（168 aa）
Not recorded NI NICKEL (II) ION × 1 BB2 ACTINONIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；10mg/ml PDF, 20mM actinonin, 50mM HEPES, pH 7.5 + 25-32% PEG 4000, 0.1M sodium citrate, pH 5.6, 0.2M ammonium acetate, VAPOR DIFFUSION, HANGING DROP at 290K
Resolution 1.75 Å R-free 0.250
1G2A THE CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE COMPLEXED WITH ACTINONIN Deposited 2000-10-18 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–168（168 aa）
Not recorded NI NICKEL (II) ION × 1 BB2 ACTINONIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；10mg/ml PDF, 20mM actinonin, 50mM HEPES, pH 7.5 + 25-32% PEG 4000, 0.1M sodium citrate, pH 5.6, 0.2M ammonium acetate, VAPOR DIFFUSION, HANGING DROP at 290K
Resolution 1.75 Å R-free 0.250
1ICJ PDF PROTEIN IS CRYSTALLIZED AS NI2+ CONTAINING FORM, COCRYSTALLIZED WITH INHIBITOR POLYETHYLENE GLYCOL (PEG) Deposited 1998-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–168（168 aa）
Chain B 1–168（168 aa）
Chain C 1–168（168 aa）
Not recorded NI NICKEL (II) ION × 3 2PE NONAETHYLENE GLYCOL × 3 SO4 SULFATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å R-free 0.230
1LRU Crystal Structure of E.coli Peptide Deformylase Complexed with Antibiotic Actinonin Deposited 2002-05-16 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–168（168 aa）
Not recorded ZN ZINC ION × 1 BB2 ACTINONIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；0.5M (NH4)2SO4, 28%PEG400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.10 Å
1LRU Crystal Structure of E.coli Peptide Deformylase Complexed with Antibiotic Actinonin Deposited 2002-05-16 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–168（168 aa）
Not recorded ZN ZINC ION × 1 BB2 ACTINONIN × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；0.5M (NH4)2SO4, 28%PEG400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.10 Å
1LRU Crystal Structure of E.coli Peptide Deformylase Complexed with Antibiotic Actinonin Deposited 2002-05-16 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–168（168 aa）
Not recorded ZN ZINC ION × 1 BB2 ACTINONIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；0.5M (NH4)2SO4, 28%PEG400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.10 Å
1LRU Crystal Structure of E.coli Peptide Deformylase Complexed with Antibiotic Actinonin Deposited 2002-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–168（168 aa）
Chain C 1–168（168 aa）
Not recorded ZN ZINC ION × 2 BB2 ACTINONIN × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；0.5M (NH4)2SO4, 28%PEG400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.10 Å
1XEM High Resolution Crystal Structure of Escherichia coli Zinc- Peptide Deformylase bound to formate Deposited 2004-09-10 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–168（168 aa）
Not recorded ZN ZINC ION × 1 FMT FORMIC ACID × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；Sodium Acetate, Sodium Formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.76 Å R-free 0.204
1XEN High Resolution Crystal Structure of Escherichia coli Iron- Peptide Deformylase Bound To Formate Deposited 2004-09-10 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–168（168 aa）
Not recorded FE FE (III) ION × 1 FMT FORMIC ACID × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；Sodium Acetate, Sodium Formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.85 Å R-free 0.218
1XEO High Resolution Crystals Structure of Cobalt- Peptide Deformylase Bound To Formate Deposited 2004-09-10 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–168（168 aa）
Not recorded CO COBALT (II) ION × 1 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；Sodium Acetate, Sodium Formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.30 Å R-free 0.215
2AI8 E.coli Polypeptide Deformylase complexed with SB-485343 Deposited 2005-07-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–168（168 aa）
Not recorded NI NICKEL (II) ION × 1 SB7 [HYDROXY(3-PHENYLPROPYL)AMINO]METHANOL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.70 Å R-free 0.226
2AI8 E.coli Polypeptide Deformylase complexed with SB-485343 Deposited 2005-07-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–168（168 aa）
Not recorded NI NICKEL (II) ION × 1 SB7 [HYDROXY(3-PHENYLPROPYL)AMINO]METHANOL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.70 Å R-free 0.226
2AI8 E.coli Polypeptide Deformylase complexed with SB-485343 Deposited 2005-07-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–168（168 aa）
Not recorded NI NICKEL (II) ION × 1 SB7 [HYDROXY(3-PHENYLPROPYL)AMINO]METHANOL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.70 Å R-free 0.226
2DEF PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 20 STRUCTURES Deposited 1997-12-15 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–147（146 aa） Fragment：ACTIVE CATALYTIC CORE, RESIDUES 1 - 147
Mutation：S1A NI NICKEL (II) ION × 1 SOLUTION NMR
NMR measurement conditions pH 7.2；318 K
Resolution not provided
2KMN Solution structure of peptide deformylase complexed with actinonin Deposited 2009-08-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–148（147 aa）
Not recorded ZN ZINC ION × 1 BB2 ACTINONIN × 1 SOLUTION NMR
NMR measurement conditions pH 7.2；310 K；Ionic strength (raw mmCIF value) 10；Pressure ambient
NMR sample composition 0.6-1.0 mM [U-100% 13C; U-100% 15N] Protein-1, 1.2 mM ACTINONIN-2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2W3T Chloro complex of the Ni-Form of E.coli deformylase Deposited 2008-11-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–169（168 aa） Fragment：RESIDUES 2-169
Not recorded NI NICKEL (II) ION × 1 CL CHLORIDE ION × 1 EOH ETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4；293 K；20.5% PEG4000, 100MM NAOAC PH 4.0, 293 K
Resolution 1.69 Å R-free 0.243
2W3U formate complex of the Ni-Form of E.coli deformylase Deposited 2008-11-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–169（168 aa） Fragment：RESIDUES 2-169
Not recorded NI NICKEL (II) ION × 1 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.1；293 K；20% PEG4000, 0.2M (NH4)2SO4, 0.1M NAOAC PH 4.1, 293 K
Resolution 1.96 Å R-free 0.285
3K6L The structure of E.coli peptide deformylase (PDF) in complex with peptidomimetic ligand BB2827 Deposited 2009-10-09 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–169（169 aa）
Not recorded NI NICKEL (II) ION × 1 2BB (2S,3R)-N~4~-[(1S)-1-(dimethylcarbamoyl)-2,2-dimethylpropyl]-N~1~,2-dihydroxy-3-(2-methylpropyl)butanediamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；20% PEG3350, 0.2M Potassium formate, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 2.15 Å R-free 0.319
3K6L The structure of E.coli peptide deformylase (PDF) in complex with peptidomimetic ligand BB2827 Deposited 2009-10-09 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–169（169 aa）
Not recorded NI NICKEL (II) ION × 1 2BB (2S,3R)-N~4~-[(1S)-1-(dimethylcarbamoyl)-2,2-dimethylpropyl]-N~1~,2-dihydroxy-3-(2-methylpropyl)butanediamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；20% PEG3350, 0.2M Potassium formate, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 2.15 Å R-free 0.319
3K6L The structure of E.coli peptide deformylase (PDF) in complex with peptidomimetic ligand BB2827 Deposited 2009-10-09 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–169（169 aa）
Not recorded NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；20% PEG3350, 0.2M Potassium formate, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 2.15 Å R-free 0.319
4AL2 peptide deformylase (Ni-form) with hydrosulfide Deposited 2012-02-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–169（168 aa）
Not recorded NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；293 K；25% PEG 4000, 200 MM NAOAC PH 4.6, 293 K, INCUBATED IN H2S ATMOSPHERE EQUILIBRATED WITH 50 MM NA2S AT PH 4.6
Resolution 2.60 Å R-free 0.298
4AL2 peptide deformylase (Ni-form) with hydrosulfide Deposited 2012-02-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–169（168 aa）
Not recorded NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；293 K；25% PEG 4000, 200 MM NAOAC PH 4.6, 293 K, INCUBATED IN H2S ATMOSPHERE EQUILIBRATED WITH 50 MM NA2S AT PH 4.6
Resolution 2.60 Å R-free 0.298
4AL2 peptide deformylase (Ni-form) with hydrosulfide Deposited 2012-02-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 2–169（168 aa）
Not recorded NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；293 K；25% PEG 4000, 200 MM NAOAC PH 4.6, 293 K, INCUBATED IN H2S ATMOSPHERE EQUILIBRATED WITH 50 MM NA2S AT PH 4.6
Resolution 2.60 Å R-free 0.298
4AL3 peptide deformylase (Co-form) with mercaptoethanol Deposited 2012-02-29 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–169（168 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CO COBALT (II) ION × 1 CL CHLORIDE ION × 1 BME BETA-MERCAPTOETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；293 K；20.5% PEG 4000, 100 MM NA-ACETATE PH 4.0, 293 K. TRANSFERRED TO 20% PEG, 50 MM ACETATE PH 6.0, THEN SOAKED WITH 10 MM MERCAPTOETHANOL
Resolution 1.98 Å R-free 0.276
4AZ4 E.coli deformylase with Co(II) and hydrosulfide Deposited 2012-06-22 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–169（168 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CO COBALT (II) ION × 1 H2S HYDROSULFURIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；293 K；2 UL PROTEIN PLUS 2 UL (20% PEG 4000, 0.1 M NAOAC PH 4.6), 293 K. SOAKED IN 10% PEG4000, 20% PEG400, 0.1 M NAOAC PH 4.6, 293 K, FOR 1 DAY. INCUBATED IN H2S ATMOSPHERE EQUILIBRATED WITH 50 MM NA2S AT PH 4.6
Resolution 1.80 Å R-free 0.221
4V5B Structure of PDF binding helix in complex with the ribosome. Deposited 2007-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 50 PDB declaration: 53-meric
Chain A5 147–162（16 aa）
Mutation：YES MG MAGNESIUM ION × 170 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 3.74 Å R-free 0.323
6IZI Crystal structure of E. coli peptide deformylase and methionine aminopeptidase fitted into the cryo-EM density map of the complex Deposited 2018-12-19 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 1–169（169 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.80 Å
7D6Z Molecular model of the cryo-EM structure of 70S ribosome in complex with peptide deformylase and trigger factor Deposited 2020-10-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric
Chain g 1–169（169 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7D80 Molecular model of the cryo-EM structure of 70S ribosome in complex with peptide deformylase, trigger factor, and methionine aminopeptidase Deposited 2020-10-06 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 57-meric
Chain 3 1–169（169 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å

30 other PDB entries and 55 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DEF_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain P； PDBConstruct 1–169； UniProt 1–169

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6iy7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6iy7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6iy7
Deposition date deposition_date2018-12-13
Structure title titleE. coli peptide deformylase crystal structure fitted into the cryo-EM density map of E. coli 70S ribosome in complex with peptide deformylase
Keywords keywordsE. coli 70S ribosome, pepdite deformylase, Nascent polypeptide exit tunnel, RIBOSOME; RIBOSOME
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.95 Å
Radius of gyration Rg (electron density) rg_electron16.37 Å
Forward intensity I(0) i06426440.00
Molecular weight molecular_weight19198.0 kDa
Excluded volume excluded_volume23698 ų
Envelope volume envelope_volume15139 ų
Hydration-shell volume shell_volume9292 ų
Envelope diameter envelope_diameter54.5 Å
Shell Rg shell_rg19.19 Å
Envelope Rg envelope_rg15.37 Å
Shape Rg shape_rg16.26 Å
Total Rg total_rg16.74 Å
Total atoms total_atoms—
Residues n_residues—
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax55.5 Å
Rg (real space) rg_real16.93 Å
Rg uncertainty (real space) rg_real_error0.30 Å
I(0) (real space) i0_real6.4260e+06
I(0) uncertainty (real space) i0_real_error7.8500e+04
Rg (reciprocal space) rg_reciprocal16.93 Å
I(0) (reciprocal space) i0_reciprocal6426000.0000
Solution quality estimate total_estimate0.8799
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.2 Å
Skewness Skewness skewness0.351
Kurtosis Kurtosis kurtosis-0.138
Angular range angular_range— – 0.4700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha975600.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.831; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.946
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)