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High Resolution Crystals Structure of Cobalt- Peptide Deformylase Bound To Formate

Method: X-RAY DIFFRACTION D_max: 53.7 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Peptide deformylase

OrganismNot specified

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 A； UniProt 1–168	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

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 1XEO	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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 ligand/ion 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 ligand/ion 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
2AI8 E.coli Polypeptide Deformylase complexed with SB-485343 Deposited 2005-07-29	Different ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 construct Different ligand/ion 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 construct Different ligand/ion 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 construct Different ligand/ion 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 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 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 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 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 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 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
6IY7 E. coli peptide deformylase crystal structure fitted into the cryo-EM density map of E. coli 70S ribosome in complex with peptide deformylase Deposited 2018-12-13	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 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 10.50 Å
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 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 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 A； PDBConstruct 1–168； UniProt 1–168

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1xeo
Deposition date deposition_date	2004-09-10
Structure title title	High Resolution Crystals Structure of Cobalt- Peptide Deformylase Bound To Formate
Keywords keywords	cobalt deformylase, formate, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	16.90 Å
Radius of gyration Rg (electron density) rg_electron	15.79 Å
Forward intensity I(0) i0	6854550.00
Molecular weight molecular_weight	18979.0 kDa
Excluded volume excluded_volume	23821 Å³
Envelope volume envelope_volume	27330 Å³
Hydration-shell volume shell_volume	14635 Å³
Envelope diameter envelope_diameter	53.1 Å
Shell Rg shell_rg	21.66 Å
Envelope Rg envelope_rg	16.16 Å
Shape Rg shape_rg	15.80 Å
Total Rg total_rg	16.83 Å
Total atoms total_atoms	1328
Residues n_residues	165
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	53.7 Å
Rg (real space) rg_real	16.81 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	6.8550e+06
I(0) uncertainty (real space) i0_real_error	8.2930e+04
Rg (reciprocal space) rg_reciprocal	16.82 Å
I(0) (reciprocal space) i0_reciprocal	6855000.0000
Solution quality estimate total_estimate	0.8150
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.2 Å
Skewness Skewness skewness	0.198
Kurtosis Kurtosis kurtosis	-0.349
Angular range angular_range	— – 0.4700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1409000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Peptide deformylase
Molecular weight formula_weight	19226.2 kDa
EC 编号 ec_number	3.5.1.88
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1553

SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRLKARA

Entity 2 Entity 2 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	223

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1xeoa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.167 — Peptide deformylase
Superfamily Superfamily superfamily	d.167.1 — Peptide deformylase
Family Family family	d.167.1.1 — Peptide deformylase

CATH v4.4 (1 domains)

Domain ID domain_id	1xeoA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	45 — Peptide Deformylase
Homologous superfamily homologous superfamily	10 — Peptide deformylase

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8. Citations (1)

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Unit-cell length a length_a	54.420 Å
Unit-cell length b length_b	54.420 Å
Unit-cell length c length_c	224.430 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	19.940 Å
R factor r_factor	0.2000
R_work r_work	0.2000
R_free r_free	0.2150

fit	/app/data/saxs_computation/xe/1xeo/1xeo.fit
pddf	/app/data/pr_computation/xe/1xeo/1xeo.pr.out
profile	/app/data/saxs_computation/xe/1xeo/1xeo.dat