SAXSdb — 9z4d

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

Cysteine--tRNA ligase

Plasmodium falciparum 3D7

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 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 A； UniProt 91–535 链 B； UniProt 91–535	片段：residues 91-535	ZN ZINC ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. Crystals were obtained as the GSU complex and soaked for 2 weeks with 10 mM Histidine in cryoprotectant. This displaced the GSU ligand resulting in an apo structure. Histidine was not bound. plate Liu-S-192 H8 , Puck: PSL-0115, Cryo: 3.4M sodium malonate	分辨率 2.87 Å R-free 0.236

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 9Z4D	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
9YRU Crystal structure of Apo Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum (Orthrhombic P form) 提交 2025-10-17	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 × 2 PDB 声明：dimeric	链 A 91–535（445 aa）片段：residues 91-535 链 B 91–535（445 aa）片段：residues 91-535	未记录	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.9；291 K；Berkeley D7: 100mM potassium phosphate dibasic, 100 mM potassium chloride, 30% PEG 3350. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 4mM ATP added to the protein prior to screening but ligand is not bound likely due to high phosphate concentration in the crystallant. plate 20147 D7 drop 1 , Puck: PSL-0309, Cryo: direct	分辨率 3.06 Å R-free 0.288
9YRW Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE 提交 2025-10-17	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 × 2 PDB 声明：dimeric	链 A 91–535（445 aa）片段：residues 91-535 链 B 91–535（445 aa）片段：residues 91-535	未记录	MLI MALONATE ION × 5 GSU O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE × 2 ZN ZINC ION × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 24 hour soak with 10 mM GSU in 3.4M sodium malonate. Liu-S-192 E1, Puck: PSL-0114, Cryo: direct from soaking solution	分辨率 2.03 Å R-free 0.200
9YRX Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with Cysteine 提交 2025-10-17	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 × 2 PDB 声明：dimeric	链 A 91–535（445 aa）片段：residues 91-535 链 B 91–535（445 aa）片段：residues 91-535	未记录	MLI MALONATE ION × 4 CYS CYSTEINE × 2 ZN ZINC ION × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 24 hour soak with 10 mM cysteine in 3.4M sodium malonate. Liu-S-192 E1, Puck: PSL-0201, Cryo: direct from soaking solution	分辨率 2.16 Å R-free 0.215
9YRZ Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with AMP 提交 2025-10-17	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 × 2 PDB 声明：dimeric	链 A 91–535（445 aa）片段：residues 91-535 链 B 91–535（445 aa）片段：residues 91-535	未记录	AMP ADENOSINE MONOPHOSPHATE × 4 MLI MALONATE ION × 5 ZN ZINC ION × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 24 hour soak with 10 mM AMP in 3.4M sodium malonate. Liu-S-192 E1, Puck: PSL-0203, Cryo: direct from soaking solution	分辨率 2.06 Å R-free 0.195
9YS0 Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with ADP 提交 2025-10-17	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 × 2 PDB 声明：dimeric	链 A 91–535（445 aa）片段：residues 91-535 链 B 91–535（445 aa）片段：residues 91-535	未记录	ADP ADENOSINE-5'-DIPHOSPHATE × 4 MLI MALONATE ION × 5 ZN ZINC ION × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 24 hour soak with 10 mM ADP in 3.4M sodium malonate. Liu-S-192 E1, Puck: PSL-0205, Cryo: direct from soaking solution	分辨率 2.14 Å R-free 0.199
9YS1 Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with AMP and Cysteine 提交 2025-10-17	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 × 2 PDB 声明：dimeric	链 A 91–535（445 aa）片段：residues 91-535 链 B 91–535（445 aa）片段：residues 91-535	未记录	CYS CYSTEINE × 2 AMP ADENOSINE MONOPHOSPHATE × 4 MLI MALONATE ION × 3 ZN ZINC ION × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 24 hour soak with 10 mM AMP and Cysteine in 3.4M sodium malonate. plate Liu-S-192 G5 Puck: PSL-0209, Cryo: direct from soaking solution	分辨率 2.34 Å R-free 0.215
9YS2 Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with cysteinyl-AMP 提交 2025-10-17	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 × 2 PDB 声明：dimeric	链 A 91–535（445 aa）片段：residues 91-535 链 B 91–535（445 aa）片段：residues 91-535	未记录	A1CYZ 5'-O-[(R)-{[(2R)-2-amino-3-sulfanylpropanoyl]oxy}(hydroxy)phosphoryl]adenosine × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MLI MALONATE ION × 5 ZN ZINC ION × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 24 hour soak with 10 mM ATP and Cysteine in 3.4M sodium malonate. The cysteinyl-AMP intermediate formed during the soak. plate Liu-S-192 G6 Puck: PSL-0210, Cryo: direct from soaking solution	分辨率 2.22 Å R-free 0.205
9YT0 Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with ADP (long soak) 提交 2025-10-20	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 × 2 PDB 声明：dimeric	链 A 91–535（445 aa）片段：residues 91-535 链 B 91–535（445 aa）片段：residues 91-535	未记录	ADP ADENOSINE-5'-DIPHOSPHATE × 4 MLI MALONATE ION × 3 ZN ZINC ION × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 1 month soak with 10 mM ADP in 3.4M sodium malonate. plate Liu-S-192 H3 Puck: PSL-2013, Cryo: direct from soaking solution	分辨率 2.45 Å R-free 0.216
9YT2 Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with ATP (long soak) 提交 2025-10-20	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 × 2 PDB 声明：dimeric	链 A 91–535（445 aa）片段：residues 91-535 链 B 91–535（445 aa）片段：residues 91-535	未记录	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MLI MALONATE ION × 3 ZN ZINC ION × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 1 month soak with 10 mM ATP in 3.4M sodium malonate. plate Liu-S-192 H3 Puck: PSL-2014, Cryo: direct from soaking solution	分辨率 2.80 Å R-free 0.225
9YT3 Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with 5'-Sulfamoyladenosine 提交 2025-10-20	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 × 2 PDB 声明：dimeric	链 A 91–535（445 aa）片段：residues 91-535 链 B 91–535（445 aa）片段：residues 91-535	未记录	LMS [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE × 3 ZN ZINC ION × 2 NA SODIUM ION × 4 CL CHLORIDE ION × 24 MLI MALONATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 7 day soak with 10 mM LMS in 3.4M sodium malonate. plate Liu-S-192 G8 Puck: PSL-2103, Cryo: direct from soaking solution	分辨率 2.77 Å R-free 0.234
9YT5 Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with GMP 提交 2025-10-20	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 × 2 PDB 声明：dimeric	链 A 91–535（445 aa）片段：residues 91-535 链 B 91–535（445 aa）片段：residues 91-535	未记录	5GP GUANOSINE-5'-MONOPHOSPHATE × 4 MLI MALONATE ION × 3 ZN ZINC ION × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 7 day soak with 10 mM GMP in 3.4M sodium malonate. plate Liu-S-192 H7 Puck: PSL-2106, Cryo: direct from soaking solution	分辨率 2.90 Å R-free 0.215

共 11 个其他 PDB 条目、11 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	Q8IJP3_PLAF7
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 22–466； UniProt 91–535 作者链 B； PDB构建体 22–466； UniProt 91–535

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。

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	9z4d
沉积日期 deposition_date	2025-11-10
最后修订 last_revision	2025-11-19
结构标题 title	Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum (Hexagonal P form)
关键词 keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, TRANSFERASE, Cysteinyl-tRNA synthetase, CysRS ;; TRANSFERASE
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	32.46 Å
回转半径 Rg (电子) rg_electron	31.90 Å
零角强度 I(0) i0	143119000.00
分子量 molecular_weight	99846.0 kDa
排除体积 excluded_volume	126320 Å³
包络体积 envelope_volume	148330 Å³
水化壳体积 shell_volume	39656 Å³
包络直径 envelope_diameter	117.5 Å
壳层 Rg shell_rg	37.83 Å
包络 Rg envelope_rg	32.09 Å
形状 Rg shape_rg	31.92 Å
总 Rg total_rg	32.29 Å
总原子数 total_atoms	7053
残基数 n_residues	856
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	113.3 Å
Rg (实空间) rg_real	34.02 Å
Rg 误差 (实空间) rg_real_error	0.45 Å
I(0) (实空间) i0_real	1.4340e+08
I(0) 误差 (实空间) i0_real_error	2.0070e+06
Rg (倒空间) rg_reciprocal	32.58 Å
I(0) (倒空间) i0_reciprocal	143100000.0000
解质量估计 total_estimate	0.6555
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	34.7 Å
偏度 Skewness skewness	0.560
峰度 Kurtosis kurtosis	-0.208
角度范围 angular_range	— – 0.2450 Å⁻¹
当前正则化参数 α current_alpha	3.0310
最高正则化参数 α highest_alpha	34480000.0000
实空间数据点数 n_real_points	50
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.776; Stabil: 0.882; Sysdev: 0.000; Positv: 1.000; Valcen: 0.901; Smooth: 0.684

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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 (5)

实体 1 Entity 1 polymer

描述 description	Cysteine--tRNA ligase
分子量 formula_weight	54533.2 kDa
EC 编号 ec_number	6.1.1.16
来源方法 src_method	man
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	7055

MAHHHHHHMGTLEAQTQGPGSLPKWNQPSKEGKKITNLFVNNSLTHSKVEFIPQEGNKIKWYACGPTVYDAAHLGHARTYVSFDIIRRILVNYFKYDVFMVINITDIDDKIIKRSVEEKIGFTELARKWEYEFWEDMKSLNVLLPTAITRVSEYVGDIVKYIEKIIENKYAYVSEEGSVYFDIDEFKKSEKHFYARMEPLSVKDENKILEGEGDLGVISKKKKNAYDFALWKSSKPNEPHWDSPWGKGRPGWHIECSTMASNILGDVLDIHSGGIDLRFPHHDNELAQSEAFFDHSQWVNYFLHSGHLHIEGLKMSKSLKNFITIKNMLTKYTSNQIRILFLLNKWDNFMNYSPNGESMVQCIEIDKSFTNFFAIILMKIKNFDLNSCNLYWSDADNKLNLLFRQTKNKIHEHFLDNFNTPDALLAIQKLITEINIYMDKEKIQIGLLLEIKHYINFIFDTFGLIY

来源 Source

来源生物 organism	Plasmodium falciparum 3D7
NCBI 分类编号 ncbi_taxonomy_id	36329
宿主生物 host_organism	Escherichia coli BL21(DE3)

实体 2 Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 3 Entity 3 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 4 Entity 4 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

实体 5 Entity 5 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	2

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8. 引用文献 (1)

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晶胞边长 a length_a	120.174 Å
晶胞边长 b length_b	120.174 Å
晶胞边长 c length_c	363.170 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	24

空间群 space_group	P 61 2 2
空间群编号 int_tables_number	178
晶系 crystal_system	—

分辨率 resolution	2.870 Å
最低分辨率 resolution_low	47.810 Å
R 因子 r_factor	0.2164
R_work r_work	0.2154
R_free r_free	0.2360

fit	/app/data/saxs_computation/z4/9z4d/9z4d.fit
pddf	/app/data/pr_computation/z4/9z4d/9z4d.pr.out
profile	/app/data/saxs_computation/z4/9z4d/9z4d.dat

Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum (Hexagonal P form)

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

Cysteine--tRNA ligase

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