← Back to search
4k9o

Crystal Structure of the Phe397Ala mutant of Benzoylformate Decarboxylase from Pseudomonas putida

Method: X-RAY DIFFRACTION Dmax: 114.1 Å Quality: GOOD
▼

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

Benzoylformate decarboxylase

Pseudomonas putida

UniProt P20906

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 2–528 Chain B； UniProt 2–528 Chain C； UniProt 2–528 Chain D； UniProt 2–528 Mutation：F397A MG MAGNESIUM ION × 2 TPP THIAMINE DIPHOSPHATE × 4 CA CALCIUM ION × 4 GOL GLYCEROL × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；22% PEG400, 150 mM calcium chloride, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K Resolution 1.89 Å R-free 0.192

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 4K9O Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BFD BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA Deposited 1998-04-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Not recorded CA CALCIUM ION × 8 MG MAGNESIUM ION × 4 TPP THIAMINE DIPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；CRYSTALS WERE GROWN AT ROOM TEMPERATURE BY HANGING-DROP VAPOR DIFFUSION AGAINST A WELL SOLUTION OF 22% (V/V) POLYETHYLENE GLYCOL WITH AN AVERAGE MOLECULAR WEIGHT OF 400 KDA (PEG 400), 0.15 M CACL2, 0.5% (V/V) MPD, 0.1 M TRISCL (PH 8.5). DROPS CONTAINED EQUAL VOLUMES (2 MICROL) OF WELL SOLUTION AND PURIFIED BENZOYLFORMATE DECARBOXYLASE [10 MG/ML IN 0.1 MM MGCL2, 0.2 MM TDP, 25 MM NAHEPES (PH 7.0)]., vapor diffusion - hanging drop
Resolution 1.60 Å R-free 0.186
1MCZ BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH AN INHIBITOR, R-MANDELATE Deposited 2002-08-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Chain B 1–528（528 aa）
Chain C 1–528（528 aa）
Chain D 1–528（528 aa）
Not recorded MG MAGNESIUM ION × 6 TPP THIAMINE DIPHOSPHATE × 4 RMN (R)-MANDELIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；CRYSTALS WERE GROWN AT ROOM TEMPERATURE BY HANGING-DROP VAPOR DIFFUSION AGAINST A WELL SOLUTION OF 20-22% PEG MME 2000, 100 mM Na citrate, pH 5.2-5.6, 0.15-0.2 M (NH4)2SO4 and 10 mM R-mandelate. DROPS CONTAINED EQUAL VOLUMES (2-4 MICROL) OF WELL SOLUTION AND PURIFIED BENZOYLFORMATE DECARBOXYLASE [20-50 MG/ML IN 0.1 MM MGCL2, 0.2 MM TDP, 15 MM NAHEPES (PH 7.0)]., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.220
1MCZ BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH AN INHIBITOR, R-MANDELATE Deposited 2002-08-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain E 1–528（528 aa）
Chain F 1–528（528 aa）
Chain G 1–528（528 aa）
Chain H 1–528（528 aa）
Not recorded MG MAGNESIUM ION × 6 TPP THIAMINE DIPHOSPHATE × 4 RMN (R)-MANDELIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；CRYSTALS WERE GROWN AT ROOM TEMPERATURE BY HANGING-DROP VAPOR DIFFUSION AGAINST A WELL SOLUTION OF 20-22% PEG MME 2000, 100 mM Na citrate, pH 5.2-5.6, 0.15-0.2 M (NH4)2SO4 and 10 mM R-mandelate. DROPS CONTAINED EQUAL VOLUMES (2-4 MICROL) OF WELL SOLUTION AND PURIFIED BENZOYLFORMATE DECARBOXYLASE [20-50 MG/ML IN 0.1 MM MGCL2, 0.2 MM TDP, 15 MM NAHEPES (PH 7.0)]., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.220
1MCZ BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH AN INHIBITOR, R-MANDELATE Deposited 2002-08-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain I 1–528（528 aa）
Chain J 1–528（528 aa）
Chain K 1–528（528 aa）
Chain L 1–528（528 aa）
Not recorded MG MAGNESIUM ION × 6 TPP THIAMINE DIPHOSPHATE × 4 RMN (R)-MANDELIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；CRYSTALS WERE GROWN AT ROOM TEMPERATURE BY HANGING-DROP VAPOR DIFFUSION AGAINST A WELL SOLUTION OF 20-22% PEG MME 2000, 100 mM Na citrate, pH 5.2-5.6, 0.15-0.2 M (NH4)2SO4 and 10 mM R-mandelate. DROPS CONTAINED EQUAL VOLUMES (2-4 MICROL) OF WELL SOLUTION AND PURIFIED BENZOYLFORMATE DECARBOXYLASE [20-50 MG/ML IN 0.1 MM MGCL2, 0.2 MM TDP, 15 MM NAHEPES (PH 7.0)]., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.220
1MCZ BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH AN INHIBITOR, R-MANDELATE Deposited 2002-08-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain M 1–528（528 aa）
Chain N 1–528（528 aa）
Chain O 1–528（528 aa）
Chain P 1–528（528 aa）
Not recorded MG MAGNESIUM ION × 6 TPP THIAMINE DIPHOSPHATE × 4 RMN (R)-MANDELIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；CRYSTALS WERE GROWN AT ROOM TEMPERATURE BY HANGING-DROP VAPOR DIFFUSION AGAINST A WELL SOLUTION OF 20-22% PEG MME 2000, 100 mM Na citrate, pH 5.2-5.6, 0.15-0.2 M (NH4)2SO4 and 10 mM R-mandelate. DROPS CONTAINED EQUAL VOLUMES (2-4 MICROL) OF WELL SOLUTION AND PURIFIED BENZOYLFORMATE DECARBOXYLASE [20-50 MG/ML IN 0.1 MM MGCL2, 0.2 MM TDP, 15 MM NAHEPES (PH 7.0)]., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.220
1PI3 E28Q mutant Benzoylformate Decarboxylase From Pseudomonas Putida Deposited 2003-05-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：E28Q MG MAGNESIUM ION × 4 CA CALCIUM ION × 12 TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；293 K；22% PEG 400, 0.15 M CaCl2, 0.5% MPD, 0.1 M TRIS-Cl (pH 8.5), 0.1 mM MgCl2, 0.2 mM TZD, 25 mM NA-HEPES (pH 7.0) VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.50
Resolution 1.20 Å R-free 0.136
1PO7 HIGH RESOLUTION STRUCTURE OF E28A MUTANT BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA Deposited 2003-06-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Not recorded MG MAGNESIUM ION × 4 CA CALCIUM ION × 12 TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.20 Å R-free 0.142
1Q6Z HIGH RESOLUTION STRUCTURE OF E28A MUTANT BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH THIAMIN THIAZOLONE DIPHOSPHATE Deposited 2003-08-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：E28A MG MAGNESIUM ION × 4 CA CALCIUM ION × 12 TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.00 Å R-free 0.140
1YNO High Resolution Structure of Benzoylformate Decarboxylase from Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate Deposited 2005-01-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–528（527 aa）
Not recorded MG MAGNESIUM ION × 4 CA CALCIUM ION × 12 TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 400,0.15 M CACL2, 0.5% (V/V) MPD, 0.1 M TRISCL (PH 8.5) , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.22 Å R-free 0.155
2FN3 High resolution structure of s26a mutant of benzoylformate decarboxylase from pseudomonas putida complexed with thiamine thiazolone diphosphate Deposited 2006-01-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：S26A MG MAGNESIUM ION × 4 CA CALCIUM ION × 12 TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 400,0.15 M CACL2, 0.5% (V/V)MPD, 0.1 M TRISCL (PH 8.5) , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.00 Å
2FWN Phosphorylation of an active site serine in a ThDP-dependent enzyme by phosphonate inactivation Deposited 2006-02-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 4 CA CALCIUM ION × 12 TPP THIAMINE DIPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；CRYSTALLIZATION CONDITIONS: PEG 400,0.15 M CACL2, 0.5% (V/V) MPD, 0.1 M HEPES (PH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.40 Å
2V3W Crystal structure of the benzoylformate decarboxylase variant L461A from Pseudomonas putida Deposited 2007-06-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Chain B 1–528（528 aa）
Chain C 1–528（528 aa）
Chain D 1–528（528 aa）
Mutation：YES Mutation：YES Mutation：YES Mutation：YES MG MAGNESIUM ION × 6 SO4 SULFATE ION × 4 TPP THIAMINE DIPHOSPHATE × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å R-free 0.228
3F6B Crystal structure of benzoylformate decarboxylase in complex with the pyridyl inhibitor PAA Deposited 2008-11-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain X 2–526（525 aa）
Not recorded MG MAGNESIUM ION × 4 8PA 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-2-[(1S,2E)-1-hydroxy-3-pyridin-3-ylprop-2-en-1-yl]-4-methyl-1,3-thiazol-3-ium × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 mM Tris-HCl pH 8.5, 150 mM CaCl2, 0.5% v/v MPD (2-methyl-2,4-pentanediol), 22% v/v PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.34 Å R-free 0.182
3F6E Crystal structure of benzoylformate decarboxylase in complex with the pyridyl inhibitor 3-PKB Deposited 2008-11-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain X 2–526（525 aa）
Not recorded MG MAGNESIUM ION × 4 8PA 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-2-[(1S,2E)-1-hydroxy-3-pyridin-3-ylprop-2-en-1-yl]-4-methyl-1,3-thiazol-3-ium × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 mM Tris-HCl pH 8.5, 150 mM CaCl2, 0.5% v/v MPD (2-methyl-2,4-pentanediol), 22% v/v PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.34 Å R-free 0.212
3FSJ Crystal structure of benzoylformate decarboxylase in complex with the inhibitor MBP Deposited 2009-01-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain X 1–528（528 aa）
Not recorded D7K 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(S)-hydroxy[(R)-hydroxy(methoxy)phosphoryl]phenylmethyl}-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 mM Tris-HCl pH 8.5, 150 mM CaCl2, 0.5% v/v MPD [2-methyl-2,4-pentanediol], 22% v/v PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.37 Å R-free 0.171
3FZN Intermediate analogue in benzoylformate decarboxylase Deposited 2009-01-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Chain B 1–528（528 aa）
Chain C 1–528（528 aa）
Chain D 1–528（528 aa）
Not recorded D7K 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(S)-hydroxy[(R)-hydroxy(methoxy)phosphoryl]phenylmethyl}-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium × 4 MG MAGNESIUM ION × 4 CL CHLORIDE ION × 11 PO4 PHOSPHATE ION × 3 PEG DI(HYDROXYETHYL)ETHER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；291 K；25% PEG 2000 w/v, 0.2M MgCl2 , pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 1.62 Å R-free 0.203
4GG1 Crystal Structure of Benzoylformate Decarboxylase Mutant L403T Deposited 2012-08-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：L403T TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 CA CALCIUM ION × 8 NA SODIUM ION × 4 GOL GLYCEROL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 mM Tris pH 8.5, 22% v/v PEG 400, 150 mM CaCl2, 0.5% v/v MPD [2-METHYL-2,4-PENTANEDIOL], VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.07 Å R-free 0.156
4GM0 Crystal Structure of Benzoylformate Decarboxylase Mutant L403N Deposited 2012-08-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：L403N TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 CA CALCIUM ION × 8 GOL GLYCEROL × 8 NA SODIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 mM Tris pH 8.5, 22% v/v PEG 400, 150 mM CaCl2, 0.5% v/v MPD [2-METHYL-2,4-PENTANEDIOL], vapor diffusion, hanging drop, temperature 298K
Resolution 1.07 Å R-free 0.151
4GM1 Crystal Structure of Benzoylformate Decarboxylase Mutant L403S Deposited 2012-08-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：L403S CA CALCIUM ION × 8 NA SODIUM ION × 4 GOL GLYCEROL × 8 TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 mM Tris pH 8.5, 22% v/v PEG 400, 150 mM CaCl2, 0.5% v/v MPD [2-METHYL-2,4-PENTANEDIOL], vapor diffusion, hanging drop, temperature 298K
Resolution 1.26 Å R-free 0.160
4GM4 Crystal Structure of Benzoylformate Decarboxylase Mutant L403I Deposited 2012-08-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：L403I CA CALCIUM ION × 8 GOL GLYCEROL × 8 TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 NA SODIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 mM Tris pH 8.5, 22% v/v PEG 400, 150 mM CaCl2, 0.5% v/v MPD [2-METHYL-2,4-PENTANEDIOL], vapor diffusion, hanging drop, temperature 298K
Resolution 1.28 Å R-free 0.159
4GP9 Crystal Structure of Benzoylformate Decarboxylase Mutant L403F Deposited 2012-08-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：L403F CA CALCIUM ION × 8 TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 GOL GLYCEROL × 8 NA SODIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 mM Tris pH 8.5, 22% v/v PEG 400, 150 mM CaCl2, 0.5% v/v MPD [2-METHYL-2,4-PENTANEDIOL], vapor diffusion, hanging drop, temperature 298K
Resolution 1.07 Å R-free 0.150
4GPE Crystal Structure of Benzoylformate Decarboxylase Mutant L403M Deposited 2012-08-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：L403M CA CALCIUM ION × 8 NA SODIUM ION × 4 GOL GLYCEROL × 8 TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 mM Tris pH 8.5, 22% v/v PEG 400, 150 mM CaCl2, 0.5% v/v MPD [2-METHYL-2,4-PENTANEDIOL], vapor diffusion, hanging drop, temperature 298K
Resolution 1.39 Å R-free 0.153
4JD5 Crystal Structure of Benzoylformate Decarboxylase Mutant L403E Deposited 2013-02-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：L403E TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 CA CALCIUM ION × 8 NA SODIUM ION × 4 GOL GLYCEROL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 MM TRIS PH 8.5, 22% V/V PEG 400, 150 MM CACL2, 0.5% V/V MPD, vapor diffusion, hanging drop, temperature 298K
Resolution 1.33 Å R-free 0.152
4JU8 Crystal Structure of the His70Phe mutant of Benzoylformate Decarboxylase from Pseudomonas putida Deposited 2013-03-24 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：H70F CA CALCIUM ION × 4 MG MAGNESIUM ION × 12 TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；22% PEG400, 150 mM calcium chloride, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.25 Å R-free 0.156
4JU9 Crystal Structure of the His70Leu mutant of Benzoylformate Decarboxylase from Pseudomonas putida Deposited 2013-03-24 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：H70L CA CALCIUM ION × 4 MG MAGNESIUM ION × 8 TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；22% PEG400, 150 mM calcium chloride, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.12 Å R-free 0.138
4JUA Crystal Structure of the His70Ser mutant of Benzoylformate Decarboxylase from Pseudomonas putida Deposited 2013-03-24 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：H70S CA CALCIUM ION × 4 TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 MG MAGNESIUM ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；22% PEG400, 150 mM calcium chloride, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.15 Å R-free 0.150
4JUB Crystal Structure of the His70Thr mutant of Benzoylformate Decarboxylase from Pseudomonas putida Deposited 2013-03-24 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Chain B 1–528（528 aa）
Chain C 1–528（528 aa）
Chain D 1–528（528 aa）
Mutation：H70T Mutation：H70T Mutation：H70T Mutation：H70T MG MAGNESIUM ION × 3 CA CALCIUM ION × 4 TPP THIAMINE DIPHOSPHATE × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；22% PEG400, 150 mM calcium chloride, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.90 Å R-free 0.203
4JUC Crystal Structure of the Ser26Met mutant of Benzoylformate Decarboxylase from Pseudomonas putida Deposited 2013-03-24 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Chain B 1–528（528 aa）
Chain C 1–528（528 aa）
Chain D 1–528（528 aa）
Mutation：S26M Mutation：S26M Mutation：S26M Mutation：S26M CA CALCIUM ION × 4 TPP THIAMINE DIPHOSPHATE × 4 GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；22% PEG400, 150 mM calcium chloride, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.30 Å R-free 0.228
4JUD Crystal Structure of the Ser26Thr mutant of Benzoylformate Decarboxylase from Pseudomonas putida Deposited 2013-03-24 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain X 1–528（528 aa）
Mutation：S26T TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 MG MAGNESIUM ION × 4 CA CALCIUM ION × 4 GOL GLYCEROL × 20 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；22% PEG400, 150 mM calcium chloride, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.65 Å R-free 0.182
4JUF Crystal Structure of His281Ala mutant of Benzoylformate Decarboxylase from Pseudomonas putida Deposited 2013-03-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–528（527 aa）
Chain B 2–528（527 aa）
Chain C 2–528（527 aa）
Chain D 2–528（527 aa）
Mutation：H281A Mutation：H281A Mutation：H281A Mutation：H281A MG MAGNESIUM ION × 2 CA CALCIUM ION × 5 TPP THIAMINE DIPHOSPHATE × 4 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；22% PEG400, 150 mM calcium chloride, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.211
4K9K Crystal Structure of the His281Tyr mutant of Benzoylformate Decarboxylase from Pseudomonas putida Deposited 2013-04-20 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–525（524 aa）
Mutation：H281Y TPP THIAMINE DIPHOSPHATE × 4 CA CALCIUM ION × 4 MG MAGNESIUM ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；22% PEG400, 150 mM calcium chloride, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.30 Å R-free 0.154
4K9L Crystal Structure of the His281Thr mutant of Benzoylformate Decarboxylase from Pseudomonas putida Deposited 2013-04-20 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–526（525 aa）
Mutation：H281T TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 CA CALCIUM ION × 4 EDO 1,2-ETHANEDIOL × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；22% PEG400, 150 mM calcium chloride, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.65 Å R-free 0.187
4K9M Crystal Structure of the His281Asn mutant of Benzoylformate Decarboxylase from Pseudomonas putida Deposited 2013-04-20 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–525（524 aa）
Mutation：H281N TPP THIAMINE DIPHOSPHATE × 4 CA CALCIUM ION × 4 MG MAGNESIUM ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；22% PEG400, 150 mM calcium chloride, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.15 Å R-free 0.151
4K9N Crystal Structure of the Ala460Ile mutant of Benzoylformate Decarboxylase from Pseudomonas putida Deposited 2013-04-20 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–525（524 aa）
Chain B 2–525（524 aa）
Chain C 2–525（524 aa）
Chain D 2–525（524 aa）
Mutation：A460I Mutation：A460I Mutation：A460I Mutation：A460I MG MAGNESIUM ION × 6 TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；22% PEG400, 150 mM calcium chloride, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.70 Å R-free 0.185
4K9P Crystal Structure of the His281Tyr/Ala460Ile Double Mutant of Benzoylformate Decarboxylase from Pseudomonas putida Deposited 2013-04-20 Different mutation/modification Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–528（527 aa）
Chain B 2–528（527 aa）
Chain C 2–528（527 aa）
Chain D 2–528（527 aa）
Mutation：H281Y/A460I Mutation：H281Y/A460I Mutation：H281Y/A460I Mutation：H281Y/A460I CA CALCIUM ION × 4 TPP THIAMINE DIPHOSPHATE × 4 MG MAGNESIUM ION × 2 GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；22% PEG400, 150 mM calcium chloride, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.24 Å R-free 0.201
4MPJ Phosphorylation of an active site threonine in the benzyolformate decarboxylase mutant S26T by phosphonate inactivation Deposited 2013-09-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：S26T Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 8 MG MAGNESIUM ION × 4 TPP THIAMINE DIPHOSPHATE × 4 GOL GLYCEROL × 12 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；22% PEG400, 150 mM calcium chloride, 150 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.50 Å R-free 0.142
4MPP Crystal Structure of Benzoylformate Decarboxylase Mutant H281Y/T377P/F397T/A460I Deposited 2013-09-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：H281Y/T377P/F397T/A460I CA CALCIUM ION × 8 NA SODIUM ION × 8 TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 GOL GLYCEROL × 12 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES sodium, 0.15 M calcium chloride, 22% v/v PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.159
4MPR Benzoylformate Decarboxylase: Is the tetramer vital for activity? Deposited 2013-09-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：R141E CA CALCIUM ION × 12 TPP THIAMINE DIPHOSPHATE × 4 GOL GLYCEROL × 12 CL CHLORIDE ION × 4 NA SODIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES sodium, 22% v/v PEG400, 0.15 M calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.40 Å R-free 0.150
4MQ5 Crystal Structure of Benzoylformate Decarboxylase Mutant A306F Deposited 2013-09-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：A306F CA CALCIUM ION × 12 TPP THIAMINE DIPHOSPHATE × 4 NA SODIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES sodium, 22% v/v PEG400, 0.15 M calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.147
4MZX Crystal Structure of Benzoylformate Decarboxylase Mutant T377L/A460Y Deposited 2013-09-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：T377L/A460Y CA CALCIUM ION × 4 GOL GLYCEROL × 8 TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 NA SODIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.15 M Tris, 22% PEG400, 0.1 M calcium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.56 Å R-free 0.150
4QEL Crystal Structure of Benzoylformate Decarboxylase Mutant H70A Deposited 2014-05-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa） Fragment：benzoylformate decarboxylase
Mutation：H70A CA CALCIUM ION × 12 CL CHLORIDE ION × 4 MG MAGNESIUM ION × 4 TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 mM TRIS , 22% PEG400, 150 mM CaCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.43 Å R-free 0.158
5DEI BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA Deposited 2015-08-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–525（524 aa）
Chain B 2–525（524 aa）
Chain C 2–525（524 aa）
Chain D 2–525（524 aa）
Not recorded BCT BICARBONATE ION × 4 TPP THIAMINE DIPHOSPHATE × 4 MG MAGNESIUM ION × 8 CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；CRYSTALS WERE GROWN AT ROOM TEMPERATURE BY HANGING-DROP VAPOR DIFFUSION AGAINST A WELL SOLUTION OF 22% (V/V) POLYETHYLENE GLYCOL WITH AN AVERAGE MOLECULAR WEIGHT OF 400 KDA (PEG 400), 0.15 M CACL2, 0.5% (V/V) MPD, 0.1 M TRISCL (PH 8.5)
Resolution 1.30 Å R-free 0.148
5DGD Benzoylformate decarboxylase F464I and A460V mutant from Pseudomonas putida Deposited 2015-08-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–525（524 aa）
Mutation：A460V, F464I MG MAGNESIUM ION × 12 CA CALCIUM ION × 12 TPP THIAMINE DIPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；24% (V/V) PEG 400, 0.15 M CACl2, 0.5% (V/V) MPD, 0.1 M TRISCL (PH 8.5)
Resolution 1.13 Å R-free 0.150
5DGT BENZOYLFORMATE DECARBOXYLASE H70A MUTANT at pH 8.5 FROM PSEUDOMONAS PUTIDA Deposited 2015-08-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–525（524 aa）
Not recorded MG MAGNESIUM ION × 4 CA CALCIUM ION × 12 TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；22% (V/V) PEG400, 0.15 M CACl2, 0.5% (V/V), MPD, 0.1 M TRISCl (pH 8.5)
Resolution 1.08 Å R-free 0.150
6M2Y Crystal structure of a formolase, BFD variant M6 from Pseudomonas putida Deposited 2020-03-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：S26F, W86R, N87T, L109S, L110E, H281Y, A460M TPP THIAMINE DIPHOSPHATE × 4 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；0.1 M acetate pH 4.5, 0.2 M NaCl,40% (v/v) PEG-300
Resolution 2.10 Å R-free 0.189
6M2Z Crystal structure of a formolase, BFD variant M3 from Pseudomonas putida Deposited 2020-03-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Mutation：W86R, N87T, L109G, L110E, A460M TPP THIAMINE DIPHOSPHATE × 4 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；0.1 M sodium acetate 4.6, 0.1 M sodium chloride, 12 % w/v PEG 6000
Resolution 2.35 Å R-free 0.249
8XBO Crystal structure of activity improved formolase variant K6 Deposited 2023-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–528（528 aa）
Not recorded TPP THIAMINE DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Na/K phosphate pH 6.2, 0.2 M NaCl, 36% (v/v) PEG-400
Resolution 2.53 Å R-free 0.244
8XBQ Crystal structure of activity improved formolase variant K1 Deposited 2023-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–528（528 aa）
Not recorded TPP THIAMINE DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium citrate 5.5, 20 % w/v PEG 3000
Resolution 2.05 Å R-free 0.241
8XBR Crystal structure of activity improved formolase variant K3 Deposited 2023-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–526（526 aa）
Not recorded TPP THIAMINE DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Na/K phosphate pH 6.2, 0.2 M NaCl , 36% (v/v) PEG-400
Resolution 1.92 Å R-free 0.178
9V67 The crystal structure of a ThDP-dependent enzyme PpBFD Deposited 2025-05-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Chain B 1–528（528 aa）
Chain C 1–528（528 aa）
Chain D 1–528（528 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.25 Å R-free 0.229
9V6F The crystal structure of a ThDP-dependent enzyme PpBFD Deposited 2025-05-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–528（528 aa）
Chain B 1–528（528 aa）
Chain C 1–528（528 aa）
Chain D 1–528（528 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.64 Å R-free 0.230

48 other PDB entries and 51 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MDLC_PSEPU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–527； UniProt 2–528 Author chain B； PDBConstruct 1–527； UniProt 2–528 Author chain C； PDBConstruct 1–527； UniProt 2–528 Author chain D； PDBConstruct 1–527； UniProt 2–528

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 4k9o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4k9o
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id4k9o
Deposition date deposition_date2013-04-20
Structure title titleCrystal Structure of the Phe397Ala mutant of Benzoylformate Decarboxylase from Pseudomonas putida
Keywords keywordsThiamine Diphosphate, LYASE; LYASE
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier36.87 Å
Radius of gyration Rg (electron density) rg_electron35.90 Å
Forward intensity I(0) i0780816000.00
Molecular weight molecular_weight225810.0 kDa
Excluded volume excluded_volume281320 ų
Envelope volume envelope_volume330610 ų
Hydration-shell volume shell_volume71684 ų
Envelope diameter envelope_diameter117.5 Å
Shell Rg shell_rg45.42 Å
Envelope Rg envelope_rg36.08 Å
Shape Rg shape_rg35.88 Å
Total Rg total_rg36.49 Å
Total atoms total_atoms15872
Residues n_residues2098
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
▼

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

Maximum dimension Dmax dmax114.1 Å
Rg (real space) rg_real36.64 Å
Rg uncertainty (real space) rg_real_error0.66 Å
I(0) (real space) i0_real7.8080e+08
I(0) uncertainty (real space) i0_real_error1.2930e+07
Rg (reciprocal space) rg_reciprocal36.78 Å
I(0) (reciprocal space) i0_reciprocal780900000.0000
Solution quality estimate total_estimate0.8249
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.8 Å
Skewness Skewness skewness0.153
Kurtosis Kurtosis kurtosis-0.496
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha476300000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

▼

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd4k9oa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.0 — automated matches
Domain ID domain_idd4k9oa2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamilyc.31.1 — DHS-like NAD/FAD-binding domain
Family Family familyc.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain
Domain ID domain_idd4k9oa3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.0 — automated matches
Domain ID domain_idd4k9ob1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.0 — automated matches
Domain ID domain_idd4k9ob2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamilyc.31.1 — DHS-like NAD/FAD-binding domain
Family Family familyc.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain
Domain ID domain_idd4k9ob3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.0 — automated matches
Domain ID domain_idd4k9oc1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.0 — automated matches
Domain ID domain_idd4k9oc2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamilyc.31.1 — DHS-like NAD/FAD-binding domain
Family Family familyc.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain
Domain ID domain_idd4k9oc3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.0 — automated matches
Domain ID domain_idd4k9od1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.0 — automated matches
Domain ID domain_idd4k9od2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamilyc.31.1 — DHS-like NAD/FAD-binding domain
Family Family familyc.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain
Domain ID domain_idd4k9od3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id4k9oA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id4k9oA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id4k9oA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id4k9oB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id4k9oB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id4k9oB03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id4k9oC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id4k9oC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id4k9oC03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id4k9oD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id4k9oD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id4k9oD03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
▶

8. Citations (1)

▶

9. Files and Curves (10)