1k4y

Crystal Structure of Rabbit Liver Carboxylesterase in Complex with 4-piperidino-piperidine

Method: X-RAY DIFFRACTION D_max: 73.8 Å Quality: REASONABLE

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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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1k4y
沉积日期 deposition_date	2001-10-09
结构标题 title	Crystal Structure of Rabbit Liver Carboxylesterase in Complex with 4-piperidino-piperidine
关键词 keywords	HYDROLASE, ESTERASE, SIDE DOOR, CAMPTOTHECIN, IRINOTECAN; HYDROLASE
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	23.81 Å
回转半径 Rg (电子) rg_electron	22.62 Å
零角强度 I(0) i0	49927900.00
分子量 molecular_weight	56718.0 kDa
排除体积 excluded_volume	71755 Å³
包络体积 envelope_volume	82473 Å³
水化壳体积 shell_volume	29374 Å³
包络直径 envelope_diameter	76.7 Å
壳层 Rg shell_rg	30.79 Å
包络 Rg envelope_rg	22.94 Å
形状 Rg shape_rg	22.58 Å
总 Rg total_rg	23.68 Å
总原子数 total_atoms	3996
残基数 n_residues	501
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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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	73.8 Å
Rg (实空间) rg_real	23.88 Å
Rg 误差 (实空间) rg_real_error	0.13 Å
I(0) (实空间) i0_real	4.8680e+07
I(0) 误差 (实空间) i0_real_error	4.6420e+05
Rg (倒空间) rg_reciprocal	23.70 Å
I(0) (倒空间) i0_reciprocal	49930000.0000
解质量估计 total_estimate	0.7054
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	30.0 Å
偏度 Skewness skewness	0.233
峰度 Kurtosis kurtosis	-0.309
角度范围 angular_range	— – 0.3350 Å⁻¹
当前正则化参数 α current_alpha	6.9310
最高正则化参数 α highest_alpha	13530000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 0.928; Sysdev: 0.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.652

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	LIVER CARBOXYLESTERASE
分子量 formula_weight	59025.6 kDa
EC 编号 ec_number	3.1.1.1
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	4379

PPVVDTVHGKVLGKFVSLEGFAQPVAVFLGVPFAKPPLGSLRFAPPQPAESWSHVKNTTSYPPMCSQDAVSGHMLSELFTNRKENIPLKFSEDCLYLNIYTPADLTKRGRLPVMVWIHGGGLMVGGASTYDGLALSAHENVVVVTIQYRLGIWGFFSTGDEHSRGNWGHLDQVAALRWVQDNIANFGGDPGSVTIFGESAGGQSVSILLLSPLTKNLFHRAISESGVALLSSLFRKNTKSLAEKIAIEAGCKTTTSAVMVHCLRQKTEEELMEVTLKMKFMALDLVGDPKENTAFLTTVIDGVLLPKAPAEILAEKKYNMLPYMVGINQQEFGWIIPMQMLGYPLSEGKLDQKTATELLWKSYPIVNVSKELTPVATEKYLGGTDDPVKKKDLFLDMLADLLFGVPSVNVARHHRDAGAPTYMYEYRYRPSFSSDMRPKTVIGDHGDEIFSVLGAPFLKEGATEEEIKLSKMVMKYWANFARNGNPNGEGLPQWPAYDYKEGYLQIGATTQAAQKLKDKEVAFWTELWAKEAAR

来源 Source

来源生物 organism	Oryctolagus cuniculus
通用名 common_name	rabbit
NCBI 分类编号 ncbi_taxonomy_id	9986
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	910.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	4-PIPERIDINO-PIPERIDINE
分子量 formula_weight	168.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	383

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6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1k4ya_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.69 — alpha/beta-Hydrolases
超家族 Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
家族 Family family	c.69.1.1 — Acetylcholinesterase-like

CATH v4.4 (1 domains)

结构域编号 domain_id	1k4yA00
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	1820 — Alpha/Beta hydrolase fold, catalytic domain

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7. 引用文献 (1)

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晶胞边长 a length_a	110.230 Å
晶胞边长 b length_b	110.230 Å
晶胞边长 c length_c	282.520 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	18

空间群 space_group	H 3 2
空间群编号 int_tables_number	155
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2290
R_work r_work	0.2290
R_free r_free	0.2940

fit	/app/data/saxs_computation/k4/1k4y/1k4y.fit
pddf	/app/data/pr_computation/k4/1k4y/1k4y.pr.out
profile	/app/data/saxs_computation/k4/1k4y/1k4y.dat