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Crystal structure of activity improved formolase variant K6

Method: X-RAY DIFFRACTION D_max: 78.7 Å Quality: EXCELLENT

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–528	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

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 8XBO	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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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：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 mutation/modification Different oligomeric state 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：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 mutation/modification Different oligomeric state 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：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 oligomeric state 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：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 oligomeric state 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：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 mutation/modification Different oligomeric state 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）	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 construct Different mutation/modification Different oligomeric state 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 oligomeric state 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：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 oligomeric state Different ligand/ion Different experimental conditions 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 oligomeric state 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：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 oligomeric state 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）	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
4K9O Crystal Structure of the Phe397Ala mutant of Benzoylformate Decarboxylase from Pseudomonas putida Deposited 2013-04-20	Different construct Different mutation/modification Different oligomeric state 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：F397A Mutation：F397A Mutation：F397A 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
4K9P Crystal Structure of the His281Tyr/Ala460Ile Double Mutant of Benzoylformate Decarboxylase from Pseudomonas putida Deposited 2013-04-20	Different construct Different mutation/modification Different oligomeric state 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：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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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
8XBQ Crystal structure of activity improved formolase variant K1 Deposited 2023-12-06	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 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 oligomeric state 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 oligomeric state 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 1–528； UniProt 1–528

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

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	8xbo
Deposition date deposition_date	2023-12-06
Structure title title	Crystal structure of activity improved formolase variant K6
Keywords keywords	formolase, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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	25.12 Å
Radius of gyration Rg (electron density) rg_electron	24.04 Å
Forward intensity I(0) i0	54351400.00
Molecular weight molecular_weight	56430.0 kDa
Excluded volume excluded_volume	70281 Å³
Envelope volume envelope_volume	81986 Å³
Hydration-shell volume shell_volume	28321 Å³
Envelope diameter envelope_diameter	80.8 Å
Shell Rg shell_rg	31.44 Å
Envelope Rg envelope_rg	24.22 Å
Shape Rg shape_rg	24.05 Å
Total Rg total_rg	24.85 Å
Total atoms total_atoms	3967
Residues n_residues	525
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	78.7 Å
Rg (real space) rg_real	25.04 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	5.4350e+07
I(0) uncertainty (real space) i0_real_error	7.1770e+05
Rg (reciprocal space) rg_reciprocal	25.07 Å
I(0) (reciprocal space) i0_reciprocal	54350000.0000
Solution quality estimate total_estimate	0.9081
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.7 Å
Skewness Skewness skewness	0.200
Kurtosis Kurtosis kurtosis	-0.572
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10010000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.991

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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	Benzoylformate decarboxylase
Molecular weight formula_weight	56421.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4088

MASVHGTTYELLRRQGIDTVFGNPGFNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNARTSHSPLIVTAGQQTRAMIGVEAGETNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYYQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGMLRQFAGLLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVSPVK

来源 Source

来源生物 organism	Pseudomonas putida
NCBI Class编号 ncbi_taxonomy_id	303
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	THIAMINE DIPHOSPHATE
Molecular weight formula_weight	425.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	121

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8. Citations (1)

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Unit-cell length a length_a	97.899 Å
Unit-cell length b length_b	99.210 Å
Unit-cell length c length_c	111.214 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.530 Å
Low-resolution limit resolution_low	49.600 Å
R factor r_factor	0.1900
R_work r_work	0.1871
R_free r_free	0.2444

fit	/app/data/saxs_computation/xb/8xbo/8xbo.fit
pddf	/app/data/pr_computation/xb/8xbo/8xbo.pr.out
profile	/app/data/saxs_computation/xb/8xbo/8xbo.dat