3fsj

Crystal structure of benzoylformate decarboxylase in complex with the inhibitor MBP

Method: X-RAY DIFFRACTION D_max: 77.9 Å Quality: EXCELLENT

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1. 蛋白身份与相关结构 Protein Identity & Related Structures

Benzoylformate decarboxylase

Pseudomonas putida

UniProt P20906

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白同源多聚体同源多聚体蛋白 × 4 PDB 声明：tetrameric（4）与蛋白拷贝数一致	链 X； UniProt 1–528	未记录	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结晶条件：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	分辨率 1.37 Å R-free 0.171

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly， “相对当前条目”直接指出证据层面的不同；没有差异标签表示当前已读取字段一致。

其他 PDB	相对当前条目 3FSJ	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
1BFD BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA 提交 1998-04-30	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	未记录	CA CALCIUM ION × 8 MG MAGNESIUM ION × 4 TPP THIAMINE DIPHOSPHATE × 4	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 1.60 Å R-free 0.186
1MCZ BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH AN INHIBITOR, R-MANDELATE 提交 2002-08-06	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）链 B 1–528（528 aa）链 C 1–528（528 aa）链 D 1–528（528 aa）	未记录	MG MAGNESIUM ION × 6 TPP THIAMINE DIPHOSPHATE × 4 RMN (R)-MANDELIC ACID × 4	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 2.80 Å R-free 0.220
1MCZ BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH AN INHIBITOR, R-MANDELATE 提交 2002-08-06	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 E 1–528（528 aa）链 F 1–528（528 aa）链 G 1–528（528 aa）链 H 1–528（528 aa）	未记录	MG MAGNESIUM ION × 6 TPP THIAMINE DIPHOSPHATE × 4 RMN (R)-MANDELIC ACID × 4	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 2.80 Å R-free 0.220
1MCZ BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH AN INHIBITOR, R-MANDELATE 提交 2002-08-06	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 3 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 I 1–528（528 aa）链 J 1–528（528 aa）链 K 1–528（528 aa）链 L 1–528（528 aa）	未记录	MG MAGNESIUM ION × 6 TPP THIAMINE DIPHOSPHATE × 4 RMN (R)-MANDELIC ACID × 4	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 2.80 Å R-free 0.220
1MCZ BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH AN INHIBITOR, R-MANDELATE 提交 2002-08-06	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 4 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 M 1–528（528 aa）链 N 1–528（528 aa）链 O 1–528（528 aa）链 P 1–528（528 aa）	未记录	MG MAGNESIUM ION × 6 TPP THIAMINE DIPHOSPHATE × 4 RMN (R)-MANDELIC ACID × 4	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 2.80 Å R-free 0.220
1PI3 E28Q mutant Benzoylformate Decarboxylase From Pseudomonas Putida 提交 2003-05-29	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：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结晶条件 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	分辨率 1.20 Å R-free 0.136
1PO7 HIGH RESOLUTION STRUCTURE OF E28A MUTANT BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA 提交 2003-06-13	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	未记录	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结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 1.20 Å R-free 0.142
1Q6Z HIGH RESOLUTION STRUCTURE OF E28A MUTANT BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH THIAMIN THIAZOLONE DIPHOSPHATE 提交 2003-08-14	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：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结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 1.00 Å R-free 0.140
1YNO High Resolution Structure of Benzoylformate Decarboxylase from Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate 提交 2005-01-24	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 2–528（527 aa）	未记录	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结晶条件 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	分辨率 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 提交 2006-01-10	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：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结晶条件 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	分辨率 1.00 Å
2FWN Phosphorylation of an active site serine in a ThDP-dependent enzyme by phosphonate inactivation 提交 2006-02-02	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	非标准单体：是（mmCIF未提供具体位点）	MG MAGNESIUM ION × 4 CA CALCIUM ION × 12 TPP THIAMINE DIPHOSPHATE × 4	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 1.40 Å
2V3W Crystal structure of the benzoylformate decarboxylase variant L461A from Pseudomonas putida 提交 2007-06-25	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）链 B 1–528（528 aa）链 C 1–528（528 aa）链 D 1–528（528 aa）	突变：YES 突变：YES 突变：YES 突变：YES	MG MAGNESIUM ION × 6 SO4 SULFATE ION × 4 TPP THIAMINE DIPHOSPHATE × 4	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 2.20 Å R-free 0.228
3F6B Crystal structure of benzoylformate decarboxylase in complex with the pyridyl inhibitor PAA 提交 2008-11-05	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 X 2–526（525 aa）	未记录	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结晶条件 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	分辨率 1.34 Å R-free 0.182
3F6E Crystal structure of benzoylformate decarboxylase in complex with the pyridyl inhibitor 3-PKB 提交 2008-11-05	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 X 2–526（525 aa）	未记录	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结晶条件 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	分辨率 1.34 Å R-free 0.212
3FZN Intermediate analogue in benzoylformate decarboxylase 提交 2009-01-26	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）链 B 1–528（528 aa）链 C 1–528（528 aa）链 D 1–528（528 aa）	未记录	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结晶条件 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	分辨率 1.62 Å R-free 0.203
4GG1 Crystal Structure of Benzoylformate Decarboxylase Mutant L403T 提交 2012-08-04	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：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结晶条件 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	分辨率 1.07 Å R-free 0.156
4GM0 Crystal Structure of Benzoylformate Decarboxylase Mutant L403N 提交 2012-08-15	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：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结晶条件 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	分辨率 1.07 Å R-free 0.151
4GM1 Crystal Structure of Benzoylformate Decarboxylase Mutant L403S 提交 2012-08-15	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：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结晶条件 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	分辨率 1.26 Å R-free 0.160
4GM4 Crystal Structure of Benzoylformate Decarboxylase Mutant L403I 提交 2012-08-15	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：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结晶条件 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	分辨率 1.28 Å R-free 0.159
4GP9 Crystal Structure of Benzoylformate Decarboxylase Mutant L403F 提交 2012-08-20	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：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结晶条件 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	分辨率 1.07 Å R-free 0.150
4GPE Crystal Structure of Benzoylformate Decarboxylase Mutant L403M 提交 2012-08-20	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：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结晶条件 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	分辨率 1.39 Å R-free 0.153
4JD5 Crystal Structure of Benzoylformate Decarboxylase Mutant L403E 提交 2013-02-23	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：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结晶条件 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	分辨率 1.33 Å R-free 0.152
4JU8 Crystal Structure of the His70Phe mutant of Benzoylformate Decarboxylase from Pseudomonas putida 提交 2013-03-24	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：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结晶条件 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	分辨率 1.25 Å R-free 0.156
4JU9 Crystal Structure of the His70Leu mutant of Benzoylformate Decarboxylase from Pseudomonas putida 提交 2013-03-24	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：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结晶条件 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	分辨率 1.12 Å R-free 0.138
4JUA Crystal Structure of the His70Ser mutant of Benzoylformate Decarboxylase from Pseudomonas putida 提交 2013-03-24	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：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结晶条件 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	分辨率 1.15 Å R-free 0.150
4JUB Crystal Structure of the His70Thr mutant of Benzoylformate Decarboxylase from Pseudomonas putida 提交 2013-03-24	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）链 B 1–528（528 aa）链 C 1–528（528 aa）链 D 1–528（528 aa）	突变：H70T 突变：H70T 突变：H70T 突变：H70T	MG MAGNESIUM ION × 3 CA CALCIUM ION × 4 TPP THIAMINE DIPHOSPHATE × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 1.90 Å R-free 0.203
4JUC Crystal Structure of the Ser26Met mutant of Benzoylformate Decarboxylase from Pseudomonas putida 提交 2013-03-24	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）链 B 1–528（528 aa）链 C 1–528（528 aa）链 D 1–528（528 aa）	突变：S26M 突变：S26M 突变：S26M 突变：S26M	CA CALCIUM ION × 4 TPP THIAMINE DIPHOSPHATE × 4 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 2.30 Å R-free 0.228
4JUD Crystal Structure of the Ser26Thr mutant of Benzoylformate Decarboxylase from Pseudomonas putida 提交 2013-03-24	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 X 1–528（528 aa）	突变：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结晶条件 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	分辨率 1.65 Å R-free 0.182
4JUF Crystal Structure of His281Ala mutant of Benzoylformate Decarboxylase from Pseudomonas putida 提交 2013-03-24	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 2–528（527 aa）链 B 2–528（527 aa）链 C 2–528（527 aa）链 D 2–528（527 aa）	突变：H281A 突变：H281A 突变：H281A 突变：H281A	MG MAGNESIUM ION × 2 CA CALCIUM ION × 5 TPP THIAMINE DIPHOSPHATE × 4 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 2.15 Å R-free 0.211
4K9K Crystal Structure of the His281Tyr mutant of Benzoylformate Decarboxylase from Pseudomonas putida 提交 2013-04-20	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 2–525（524 aa）	突变：H281Y	TPP THIAMINE DIPHOSPHATE × 4 CA CALCIUM ION × 4 MG MAGNESIUM ION × 12	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 1.30 Å R-free 0.154
4K9L Crystal Structure of the His281Thr mutant of Benzoylformate Decarboxylase from Pseudomonas putida 提交 2013-04-20	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 2–526（525 aa）	突变：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结晶条件 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	分辨率 1.65 Å R-free 0.187
4K9M Crystal Structure of the His281Asn mutant of Benzoylformate Decarboxylase from Pseudomonas putida 提交 2013-04-20	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 2–525（524 aa）	突变：H281N	TPP THIAMINE DIPHOSPHATE × 4 CA CALCIUM ION × 4 MG MAGNESIUM ION × 12	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 1.15 Å R-free 0.151
4K9N Crystal Structure of the Ala460Ile mutant of Benzoylformate Decarboxylase from Pseudomonas putida 提交 2013-04-20	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 2–525（524 aa）链 B 2–525（524 aa）链 C 2–525（524 aa）链 D 2–525（524 aa）	突变：A460I 突变：A460I 突变：A460I 突变：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结晶条件 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	分辨率 1.70 Å R-free 0.185
4K9O Crystal Structure of the Phe397Ala mutant of Benzoylformate Decarboxylase from Pseudomonas putida 提交 2013-04-20	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 2–528（527 aa）链 B 2–528（527 aa）链 C 2–528（527 aa）链 D 2–528（527 aa）	突变：F397A 突变：F397A 突变：F397A 突变：F397A	MG MAGNESIUM ION × 2 TPP THIAMINE DIPHOSPHATE × 4 CA CALCIUM ION × 4 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 1.89 Å R-free 0.192
4K9P Crystal Structure of the His281Tyr/Ala460Ile Double Mutant of Benzoylformate Decarboxylase from Pseudomonas putida 提交 2013-04-20	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 2–528（527 aa）链 B 2–528（527 aa）链 C 2–528（527 aa）链 D 2–528（527 aa）	突变：H281Y/A460I 突变：H281Y/A460I 突变：H281Y/A460I 突变：H281Y/A460I	CA CALCIUM ION × 4 TPP THIAMINE DIPHOSPHATE × 4 MG MAGNESIUM ION × 2 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 2.24 Å R-free 0.201
4MPJ Phosphorylation of an active site threonine in the benzyolformate decarboxylase mutant S26T by phosphonate inactivation 提交 2013-09-12	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：S26T 非标准单体：是（mmCIF未提供具体位点）	CA CALCIUM ION × 8 MG MAGNESIUM ION × 4 TPP THIAMINE DIPHOSPHATE × 4 GOL GLYCEROL × 12 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 1.50 Å R-free 0.142
4MPP Crystal Structure of Benzoylformate Decarboxylase Mutant H281Y/T377P/F397T/A460I 提交 2013-09-13	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：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结晶条件 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	分辨率 1.50 Å R-free 0.159
4MPR Benzoylformate Decarboxylase: Is the tetramer vital for activity? 提交 2013-09-13	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：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结晶条件 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	分辨率 1.40 Å R-free 0.150
4MQ5 Crystal Structure of Benzoylformate Decarboxylase Mutant A306F 提交 2013-09-15	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：A306F	CA CALCIUM ION × 12 TPP THIAMINE DIPHOSPHATE × 4 NA SODIUM ION × 8	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 1.50 Å R-free 0.147
4MZX Crystal Structure of Benzoylformate Decarboxylase Mutant T377L/A460Y 提交 2013-09-30	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：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结晶条件 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	分辨率 1.56 Å R-free 0.150
4QEL Crystal Structure of Benzoylformate Decarboxylase Mutant H70A 提交 2014-05-16	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）片段：benzoylformate decarboxylase	突变：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结晶条件 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	分辨率 1.43 Å R-free 0.158
5DEI BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA 提交 2015-08-25	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 2–525（524 aa）链 B 2–525（524 aa）链 C 2–525（524 aa）链 D 2–525（524 aa）	未记录	BCT BICARBONATE ION × 4 TPP THIAMINE DIPHOSPHATE × 4 MG MAGNESIUM ION × 8 CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray结晶条件 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)	分辨率 1.30 Å R-free 0.148
5DGD Benzoylformate decarboxylase F464I and A460V mutant from Pseudomonas putida 提交 2015-08-27	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 2–525（524 aa）	突变：A460V, F464I	MG MAGNESIUM ION × 12 CA CALCIUM ION × 12 TPP THIAMINE DIPHOSPHATE × 4	X-RAY DIFFRACTION X-ray结晶条件 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)	分辨率 1.13 Å R-free 0.150
5DGT BENZOYLFORMATE DECARBOXYLASE H70A MUTANT at pH 8.5 FROM PSEUDOMONAS PUTIDA 提交 2015-08-28	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 2–525（524 aa）	未记录	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结晶条件 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)	分辨率 1.08 Å R-free 0.150
6M2Y Crystal structure of a formolase, BFD variant M6 from Pseudomonas putida 提交 2020-03-02	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：S26F, W86R, N87T, L109S, L110E, H281Y, A460M	TPP THIAMINE DIPHOSPHATE × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；0.1 M acetate pH 4.5, 0.2 M NaCl,40% (v/v) PEG-300	分辨率 2.10 Å R-free 0.189
6M2Z Crystal structure of a formolase, BFD variant M3 from Pseudomonas putida 提交 2020-03-02	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）	突变：W86R, N87T, L109G, L110E, A460M	TPP THIAMINE DIPHOSPHATE × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 2.35 Å R-free 0.249
8XBO Crystal structure of activity improved formolase variant K6 提交 2023-12-06	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–528（528 aa）	未记录	TPP THIAMINE DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Na/K phosphate pH 6.2, 0.2 M NaCl, 36% (v/v) PEG-400	分辨率 2.53 Å R-free 0.244
8XBQ Crystal structure of activity improved formolase variant K1 提交 2023-12-06	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–528（528 aa）	未记录	TPP THIAMINE DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium citrate 5.5, 20 % w/v PEG 3000	分辨率 2.05 Å R-free 0.241
8XBR Crystal structure of activity improved formolase variant K3 提交 2023-12-06	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–526（526 aa）	未记录	TPP THIAMINE DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Na/K phosphate pH 6.2, 0.2 M NaCl , 36% (v/v) PEG-400	分辨率 1.92 Å R-free 0.178
9V67 The crystal structure of a ThDP-dependent enzyme PpBFD 提交 2025-05-26	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）链 B 1–528（528 aa）链 C 1–528（528 aa）链 D 1–528（528 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 2.25 Å R-free 0.229
9V6F The crystal structure of a ThDP-dependent enzyme PpBFD 提交 2025-05-27	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–528（528 aa）链 B 1–528（528 aa）链 C 1–528（528 aa）链 D 1–528（528 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 2.64 Å R-free 0.230

共 48 个其他 PDB 条目、51 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	MDLC_PSEPU
Isoform	—
PDB实体	1
链与序列区间	作者链 X； PDB构建体 1–528； UniProt 1–528

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

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

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	3fsj
沉积日期 deposition_date	2009-01-09
结构标题 title	Crystal structure of benzoylformate decarboxylase in complex with the inhibitor MBP
关键词 keywords	;THIAMIN ADDUCT, AROMATIC HYDROCARBONS CATABOLISM, CALCIUM, DECARBOXYLASE, LYASE, MAGNESIUM, MANDELATE PATHWAY, METAL BINDING, THIAMINE PYROPHOSPHATE, Metal-binding ;; LYASE
实验方法 method	X-RAY DIFFRACTION

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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	25.11 Å
回转半径 Rg (电子) rg_electron	24.01 Å
零角强度 I(0) i0	54391600.00
分子量 molecular_weight	56544.0 kDa
排除体积 excluded_volume	70423 Å³
包络体积 envelope_volume	82543 Å³
水化壳体积 shell_volume	28441 Å³
包络直径 envelope_diameter	81.0 Å
壳层 Rg shell_rg	31.53 Å
包络 Rg envelope_rg	24.27 Å
形状 Rg shape_rg	24.01 Å
总 Rg total_rg	24.84 Å
总原子数 total_atoms	3975
残基数 n_residues	525
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	77.9 Å
Rg (实空间) rg_real	25.02 Å
Rg 误差 (实空间) rg_real_error	0.44 Å
I(0) (实空间) i0_real	5.4390e+07
I(0) 误差 (实空间) i0_real_error	7.6860e+05
Rg (倒空间) rg_reciprocal	25.05 Å
I(0) (倒空间) i0_reciprocal	54390000.0000
解质量估计 total_estimate	0.9085
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	28.4 Å
偏度 Skewness skewness	0.205
峰度 Kurtosis kurtosis	-0.567
角度范围 angular_range	— – 0.3150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	10260000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.971

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5. 晶体学与实验 5. Crystallography & Experiment

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6. 实体与聚合物信息 Entities & Polymers (4)

实体 1 Entity 1 polymer

描述 description	Benzoylformate decarboxylase
分子量 formula_weight	56402.7 kDa
EC 编号 ec_number	4.1.1.7
来源方法 src_method	man
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	X
原子数 atom_count	4465

MASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVSPVK

来源 Source

来源生物 organism	Pseudomonas putida
NCBI 分类编号 ncbi_taxonomy_id	303
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 non-polymer

描述 description	;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 ;
分子量 formula_weight	625.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 3 Entity 3 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 4 Entity 4 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	485

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7. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d3fsjx1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.5 — Pyruvate oxidase and decarboxylase Pyr module

结构域编号 domain_id	d3fsjx2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.31 — DHS-like NAD/FAD-binding domain
超家族 Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
家族 Family family	c.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain

结构域编号 domain_id	d3fsjx3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.9 — Pyruvate oxidase and decarboxylase PP module

CATH v4.4 (3 domains)

结构域编号 domain_id	3fsjX01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	3fsjX02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1220 — TPP-binding domain

结构域编号 domain_id	3fsjX03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

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8. 引用文献 (1)

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晶胞边长 a length_a	81.484 Å
晶胞边长 b length_b	95.354 Å
晶胞边长 c length_c	137.139 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	I 2 2 2
空间群编号 int_tables_number	23
晶系 crystal_system	—

分辨率 resolution	1.370 Å
最低分辨率 resolution_low	30.980 Å
R 因子 r_factor	0.1610
R_work r_work	0.1590
R_free r_free	0.1710

fit	/app/data/saxs_computation/fs/3fsj/3fsj.fit
pddf	/app/data/pr_computation/fs/3fsj/3fsj.pr.out
profile	/app/data/saxs_computation/fs/3fsj/3fsj.dat