2akw

Crystal Structure of T.Thermophilus Phenylalanyl-tRNA synthetase complexed with p-Cl-Phenylalanine

Method: X-RAY DIFFRACTION D_max: 136.8 Å Quality: GOOD

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

Phenylalanyl-tRNA synthetase alpha chain

物种未注明

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	蛋白异源复合物异源复合物蛋白 × 4 PDB 声明：tetrameric（4）与蛋白拷贝数一致	链 A； UniProt 85–350	未记录	Phenylalanyl-tRNA synthetase beta chain × 2 （P27002） MN MANGANESE (II) ION × 2 200 4-CHLORO-L-PHENYLALANINE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；20mM Imidazole-HCl (pH 7.2), 27% (NH4)2SO4, 1mM MgCl2, 1mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	分辨率 2.80 Å R-free 0.234

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 2AKW	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
1B70 PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINE 提交 1999-01-26	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 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 A 1–350（350 aa）片段：ALPHA SUBUNIT	未记录	MG MAGNESIUM ION × 2 PHE PHENYLALANINE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；313 K；CRYSTALS WERE GROWN BY THE HANGING-DROP TECHNIQUE AT 4O C WITH AMMONIUM SULFATE AS PRECIPITANT. EACH DROPLET OF THE PHENYLALANYL-TRNA SYNTHETASE SOLUTION (10 M L) AT A PROTEIN CONCENTRTION OF 3 TO 5 MG PER ML IN 20 AMM IMIDASOL-HCL BUFFER (PH 7.8), 1 MM MGCL2, 1 MM NAN3 AND 15% SATURATED AMMONIUM SULFATE WAS EQUILIBRATED WITH 1 ML 25 TO 30% SATURATED AMMONIUM SULFATE IN THE SAME BUFFER. CRYSTALS APPEARED AFTER ONE TO TWO WEEKS AND GREW UP TO MAXIMAL DIMENSIONS (0.4MMX0.4MMX0.25 MM) IN A FEW WEEKS., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 313K	分辨率 2.70 Å R-free 0.256
1B7Y PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINYL-ADENYLATE 提交 1999-01-26	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 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 A 1–350（350 aa）	未记录	MG MAGNESIUM ION × 2 FYA ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE] × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；313 K；HANGING-DROP TECHNIQUE AT 4O C WITH (NH4)2SO4 AS PRECIPITANT. EACH DROPLET OF THE PHENYLALANYL-TRNA SYNTHETASE SOLUTION (10 microliters) AT PROTEIN CONCENTRATION OF 3 TO 5 MG PER ML IN 20 MM IMIDASOL-HCL BUFFER (PH 7.8), 1 MM MGCL2, 1 MM NAN3 AND 15% SATURATED (NH4)2SO4 IN THE SAME BUFFER. CRYSTALS APPEARED AFTER ONE TO TWO WEEKS AND GREW UP TO THE MAXIMAL DIMENSIONS OF 0.4X0.4X0.25 MM IN A FEW WEEKS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 313K	分辨率 2.50 Å R-free 0.267
1EIY THE CRYSTAL STRUCTURE OF PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH COGNATE TRNAPHE 提交 2000-02-29	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–RNA 异源复合物；蛋白 × 4 PDB 声明：hexameric	链 A 1–350（350 aa）片段：ALPHA CHAIN	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；ammonium sulphate, magnesium sulphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP at 293K	分辨率 3.30 Å R-free 0.287
2ALY Crystal Structure of T.Thermophilus Phenylalanyl-tRNA synthetase complexed with 5'-O-[N-(L-tyrosyl)sulphamoyl]adenosine 提交 2005-08-04	配体/离子不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 A 85–350（266 aa）	未记录	MN MANGANESE (II) ION × 2 YSA 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；20mM Imidazole-HCl (pH 7.2), 27% (NH4)2SO4, 1mM MgCl2, 1mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	分辨率 2.60 Å R-free 0.246
2AMC Crystal structure of Phenylalanyl-tRNA synthetase complexed with L-tyrosine 提交 2005-08-09	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 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 A 85–350（266 aa）片段：residues 85-350	未记录	MG MAGNESIUM ION × 2 TYR TYROSINE × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；20 mM Imidazole-HCl, pH 7.2, 27% (NH4)2SO4, 1mM MgCl2, 1mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	分辨率 2.70 Å R-free 0.255
2IY5 PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS complexed with tRNA and a phenylalanyl-adenylate analog 提交 2006-07-12	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–RNA 异源复合物；蛋白 × 4 PDB 声明：hexameric	链 A 1–350（350 aa）	未记录	FYA ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE] × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.8；277 K；20 MM IMIDAZOLE-HCL, PH 7.8, 1 MM MGCL2, 5 MM 2-MERCAPTOETHANOL AND 1 MM NAN3	分辨率 3.10 Å R-free 0.299
3HFZ Crystal structure of Thermus thermophilus Phenylalanyl-tRNA synthetase complexed with m-tyrosine 提交 2009-05-13	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 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 A 1–350（350 aa）	未记录	MTY META-TYROSINE × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.8；292 K；30% (NH4)2SO4, 0.02M IMIDAZOLE-HCL, 0.001M magnesium chloride, m-tyrosine, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K	分辨率 2.90 Å R-free 0.282
3TEH Crystal structure of Thermus thermophilus Phenylalanyl-tRNA synthetase complexed with L-dopa 提交 2011-08-14	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 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 A 1–350（350 aa）	未记录	DAH 3,4-DIHYDROXYPHENYLALANINE × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.8；292 K；30% (NH4)2SO4, 0.02M IMIDAZOLE-HCL, 0.001M magnesium chloride, L-dopa, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K	分辨率 2.85 Å R-free 0.297
4TVA Universal Pathway for Post-Transfer Editing Reactions: Insight from Crystal structure of TthPheRS with Puromycine 提交 2014-06-26	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 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 A 1–350（350 aa）	未记录	PHE PHENYLALANINE × 2 PUY PUROMYCIN × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.7；277 K；PROTEIN WAS CRYSTALLIZED FROM AMMONIUM SULFATE 28% OF SATURATION, 20 MM IMIDAZOLE, PH 7.7, 10 MM MGCL2, 1 MM NAN3	分辨率 2.60 Å R-free 0.258

共 9 个其他 PDB 条目、9 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	SYFA_THETH
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–266； UniProt 85–350

Phenylalanyl-tRNA synthetase beta chain

物种未注明

UniProt P27002

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	蛋白异源复合物异源复合物蛋白 × 4 PDB 声明：tetrameric（4）与蛋白拷贝数一致	链 B； UniProt 1–785	未记录	Phenylalanyl-tRNA synthetase alpha chain × 2 （P27001） MN MANGANESE (II) ION × 2 200 4-CHLORO-L-PHENYLALANINE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；20mM Imidazole-HCl (pH 7.2), 27% (NH4)2SO4, 1mM MgCl2, 1mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	分辨率 2.80 Å R-free 0.234

数据库中的同蛋白其他状态

其他 PDB	相对当前条目 2AKW	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
1B70 PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINE 提交 1999-01-26	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 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 B 1–785（785 aa）片段：BETA SUBUNIT	未记录	MG MAGNESIUM ION × 2 PHE PHENYLALANINE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；313 K；CRYSTALS WERE GROWN BY THE HANGING-DROP TECHNIQUE AT 4O C WITH AMMONIUM SULFATE AS PRECIPITANT. EACH DROPLET OF THE PHENYLALANYL-TRNA SYNTHETASE SOLUTION (10 M L) AT A PROTEIN CONCENTRTION OF 3 TO 5 MG PER ML IN 20 AMM IMIDASOL-HCL BUFFER (PH 7.8), 1 MM MGCL2, 1 MM NAN3 AND 15% SATURATED AMMONIUM SULFATE WAS EQUILIBRATED WITH 1 ML 25 TO 30% SATURATED AMMONIUM SULFATE IN THE SAME BUFFER. CRYSTALS APPEARED AFTER ONE TO TWO WEEKS AND GREW UP TO MAXIMAL DIMENSIONS (0.4MMX0.4MMX0.25 MM) IN A FEW WEEKS., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 313K	分辨率 2.70 Å R-free 0.256
1B7Y PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINYL-ADENYLATE 提交 1999-01-26	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 B 1–785（785 aa）	未记录	MG MAGNESIUM ION × 2 FYA ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE] × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；313 K；HANGING-DROP TECHNIQUE AT 4O C WITH (NH4)2SO4 AS PRECIPITANT. EACH DROPLET OF THE PHENYLALANYL-TRNA SYNTHETASE SOLUTION (10 microliters) AT PROTEIN CONCENTRATION OF 3 TO 5 MG PER ML IN 20 MM IMIDASOL-HCL BUFFER (PH 7.8), 1 MM MGCL2, 1 MM NAN3 AND 15% SATURATED (NH4)2SO4 IN THE SAME BUFFER. CRYSTALS APPEARED AFTER ONE TO TWO WEEKS AND GREW UP TO THE MAXIMAL DIMENSIONS OF 0.4X0.4X0.25 MM IN A FEW WEEKS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 313K	分辨率 2.50 Å R-free 0.267
2ALY Crystal Structure of T.Thermophilus Phenylalanyl-tRNA synthetase complexed with 5'-O-[N-(L-tyrosyl)sulphamoyl]adenosine 提交 2005-08-04	配体/离子不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 B 1–785（785 aa）	未记录	MN MANGANESE (II) ION × 2 YSA 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；20mM Imidazole-HCl (pH 7.2), 27% (NH4)2SO4, 1mM MgCl2, 1mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	分辨率 2.60 Å R-free 0.246
2AMC Crystal structure of Phenylalanyl-tRNA synthetase complexed with L-tyrosine 提交 2005-08-09	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 B 1–785（785 aa）	未记录	MG MAGNESIUM ION × 2 TYR TYROSINE × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；20 mM Imidazole-HCl, pH 7.2, 27% (NH4)2SO4, 1mM MgCl2, 1mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	分辨率 2.70 Å R-free 0.255
2IY5 PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS complexed with tRNA and a phenylalanyl-adenylate analog 提交 2006-07-12	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–RNA 异源复合物；蛋白 × 4 PDB 声明：hexameric	链 B 1–785（785 aa）	未记录	FYA ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE] × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.8；277 K；20 MM IMIDAZOLE-HCL, PH 7.8, 1 MM MGCL2, 5 MM 2-MERCAPTOETHANOL AND 1 MM NAN3	分辨率 3.10 Å R-free 0.299
3HFZ Crystal structure of Thermus thermophilus Phenylalanyl-tRNA synthetase complexed with m-tyrosine 提交 2009-05-13	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 B 1–785（785 aa）	未记录	MTY META-TYROSINE × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.8；292 K；30% (NH4)2SO4, 0.02M IMIDAZOLE-HCL, 0.001M magnesium chloride, m-tyrosine, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K	分辨率 2.90 Å R-free 0.282
3TEH Crystal structure of Thermus thermophilus Phenylalanyl-tRNA synthetase complexed with L-dopa 提交 2011-08-14	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 B 1–785（785 aa）	未记录	DAH 3,4-DIHYDROXYPHENYLALANINE × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.8；292 K；30% (NH4)2SO4, 0.02M IMIDAZOLE-HCL, 0.001M magnesium chloride, L-dopa, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K	分辨率 2.85 Å R-free 0.297
4TVA Universal Pathway for Post-Transfer Editing Reactions: Insight from Crystal structure of TthPheRS with Puromycine 提交 2014-06-26	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 B 1–785（785 aa）	未记录	PHE PHENYLALANINE × 2 PUY PUROMYCIN × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.7；277 K；PROTEIN WAS CRYSTALLIZED FROM AMMONIUM SULFATE 28% OF SATURATION, 20 MM IMIDAZOLE, PH 7.7, 10 MM MGCL2, 1 MM NAN3	分辨率 2.60 Å R-free 0.258

共 8 个其他 PDB 条目、8 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	SYFB_THETH
Isoform	—
PDB实体	2
链与序列区间	作者链 B； PDB构建体 1–785； UniProt 1–785

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	2akw
沉积日期 deposition_date	2005-08-04
结构标题 title	Crystal Structure of T.Thermophilus Phenylalanyl-tRNA synthetase complexed with p-Cl-Phenylalanine
关键词 keywords	protein-unnatural amino acid complex, LIGASE; LIGASE
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	38.34 Å
回转半径 Rg (电子) rg_electron	38.48 Å
零角强度 I(0) i0	197013000.00
分子量 molecular_weight	116850.0 kDa
排除体积 excluded_volume	147670 Å³
包络体积 envelope_volume	196280 Å³
水化壳体积 shell_volume	44862 Å³
包络直径 envelope_diameter	141.6 Å
壳层 Rg shell_rg	41.48 Å
包络 Rg envelope_rg	39.08 Å
形状 Rg shape_rg	38.47 Å
总 Rg total_rg	38.71 Å
总原子数 total_atoms	8269
残基数 n_residues	1051
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	136.8 Å
Rg (实空间) rg_real	38.79 Å
Rg 误差 (实空间) rg_real_error	1.33 Å
I(0) (实空间) i0_real	1.9700e+08
I(0) 误差 (实空间) i0_real_error	3.8150e+06
Rg (倒空间) rg_reciprocal	38.51 Å
I(0) (倒空间) i0_reciprocal	197000000.0000
解质量估计 total_estimate	0.8085
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	36.7 Å
偏度 Skewness skewness	0.625
峰度 Kurtosis kurtosis	0.001
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	37470000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.712; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.828; Smooth: 0.541

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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 (6)

实体 1 Entity 1 polymer

描述 description	Phenylalanyl-tRNA synthetase alpha chain
分子量 formula_weight	29955.4 kDa
EC 编号 ec_number	6.1.1.20
来源方法 src_method	nat
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	8466

RVDVSLPGASLFSGGLHPITLMERELVEIFRALGYQAVEGPEVESEFFNFDALNIPEHHPARDMWDTFWLTGEGFRLEGPLGEEVEGRLLLRTHTSPMQVRYMVAHTPPFRIVVPGRVFRFEQTDATHEAVFHQLEGLVVGEGIAMAHLKGAIYELAQALFGPDSKVRFQPVYFPFVEPGAQFAVWWPEGGKWLELGGAGMVHPKVFQAVDAYRERLGLPPAYRGVTGFAFGLGVERLAMLRYGIPDIRYFFGGRLKFLEQFKGVL

实体 2 Entity 2 polymer

描述 description	Phenylalanyl-tRNA synthetase beta chain
分子量 formula_weight	86720.7 kDa
EC 编号 ec_number	6.1.1.20
来源方法 src_method	nat
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	B

MRVPFSWLKAYVPELESPEVLEERLAGLGFETDRIERVFPIPRGVVFARVLEAHPIPGTRLKRLVLDAGRTVEVVSGAENARKGIGVALALPGTELPGLGQKVGERVIQGVRSFGMALSPRELGVGEYGGGLLEFPEDALPPGTPLSEAWPEEVVLDLEVTPNRPDALGLLGLARDLHALGYALVEPEAALKAEALPLPFALKVEDPEGAPHFTLGYAFGLRVAPSPLWMQRALFAAGMRPINNVVDVTNYVMLERAQPMHAFDLRFVGEGIAVRRAREGERLKTLDGVERTLHPEDLVIAGWRGEESFPLGLAGVMGGAESEVREDTEAIALEVACFDPVSIRKTARRHGLRTEASHRFERGVDPLGQVPAQRRALSLLQALAGARVAEALLEAGSPKPPEAIPFRPEYANRLLGTSYPEAEQIAILKRLGCRVEGEGPTYRVTPPSHRLDLRLEEDLVEEVARIQGYETIPLALPAFFPAPDNRGVEAPYRKEQRLREVLSGLGFQEVYTYSFMDPEDARRFRLDPPRLLLLNPLAPEKAALRTHLFPGLVRVLKENLDLDRPERALLFEVGRVFREREETHLAGLLFGEGVGLPWAKERLSGYFLLKGYLEALFARLGLAFRVEAQAFPFLHPGVSGRVLVEGEEVGFLGALHPEIAQELELPPVHLFELRLPLPDKPLAFQDPSRHPAAFRDLAVVVPAPTPYGEVEALVREAAGPYLESLALFDLYQGPPLPEGHKSLAFHLRFRHPKRTLRDEEVEEAVSRVAEALRARGFGLRGLDTP

实体 3 Entity 3 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 4 Entity 4 non-polymer

描述 description	4-CHLORO-L-PHENYLALANINE
分子量 formula_weight	199.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 5 Entity 5 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 6 Entity 6 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	197

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7. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

结构域编号 domain_id	d2akwa_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.104 — Class II aaRS and biotin synthetases
超家族 Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
家族 Family family	d.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

结构域编号 domain_id	d2akwb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.6 — Putative DNA-binding domain
超家族 Superfamily superfamily	a.6.1 — Putative DNA-binding domain
家族 Family family	a.6.1.1 — Domains B1 and B5 of PheRS-beta, PheT

结构域编号 domain_id	d2akwb2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.6 — Putative DNA-binding domain
超家族 Superfamily superfamily	a.6.1 — Putative DNA-binding domain
家族 Family family	a.6.1.1 — Domains B1 and B5 of PheRS-beta, PheT

结构域编号 domain_id	d2akwb3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.4 — Myf domain

结构域编号 domain_id	d2akwb4
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.153 — PheT/TilS domain
超家族 Superfamily superfamily	b.153.1 — PheT/TilS domain
家族 Family family	b.153.1.1 — B3/B4 domain of PheRS, PheT

结构域编号 domain_id	d2akwb5
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.13 — Anticodon-binding domain of PheRS
家族 Family family	d.58.13.1 — Anticodon-binding domain of PheRS

结构域编号 domain_id	d2akwb6
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.104 — Class II aaRS and biotin synthetases
超家族 Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
家族 Family family	d.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

CATH v4.4 (7 domains)

结构域编号 domain_id	2akwA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	930 — BirA Bifunctional Protein; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

结构域编号 domain_id	2akwB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2akwB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	2akwB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	40 — Phenylalanyl-tRNA Synthetase; Chain B, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Phenylalanyl-trna Synthetase, Chain B, domain 3

结构域编号 domain_id	2akwB04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2akwB05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	930 — BirA Bifunctional Protein; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

结构域编号 domain_id	2akwB06
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	380 — Ferrodoxin-fold anticodon-binding domain

▶

8. 引用文献 (1)

▶

晶胞边长 a length_a	172.980 Å
晶胞边长 b length_b	172.980 Å
晶胞边长 c length_c	138.510 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	120.00 °
晶胞分子数 Z z_pdb	6

空间群 space_group	P 32 2 1
空间群编号 int_tables_number	154
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	9.990 Å
R 因子 r_factor	0.2620
R_work r_work	0.2290
R_free r_free	0.2340

fit	/app/data/saxs_computation/ak/2akw/2akw.fit
pddf	/app/data/pr_computation/ak/2akw/2akw.pr.out
profile	/app/data/saxs_computation/ak/2akw/2akw.dat

Crystal Structure of T.Thermophilus Phenylalanyl-tRNA synthetase complexed with p-Cl-Phenylalanine

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

Phenylalanyl-tRNA synthetase alpha chain

当前结构中的状态

数据库中的同蛋白其他状态

Phenylalanyl-tRNA synthetase beta chain

当前结构中的状态

数据库中的同蛋白其他状态

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

2. 结构基本信息 2. Structure Basics

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

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

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

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

6. 实体与聚合物信息 Entities & Polymers (6)

实体 1 Entity 1 polymer

聚合物 Polymer

实体 2 Entity 2 polymer

聚合物 Polymer

实体 3 Entity 3 non-polymer

实体 4 Entity 4 non-polymer

实体 5 Entity 5 non-polymer

实体 6 Entity 6 water

7. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

8. 引用文献 (1)

9. 文件与曲线 (10)

Files (7)

Curves (3)