2bmk

Fab fragment of PLP-dependent catalytic antibody 15A9 in complex with phosphopyridoxyl-D-alanine

Method: X-RAY DIFFRACTION D_max: 110.6 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	2bmk
沉积日期 deposition_date	2005-03-14
结构标题 title	Fab fragment of PLP-dependent catalytic antibody 15A9 in complex with phosphopyridoxyl-D-alanine
关键词 keywords	CATALYTIC ANTIBODY, TRANSAMINATION, PYRIDOXAL-PHOSPHATE, HAPTEN, PHOSPHOPYRIDOXYL-L-LYSINE, IMMUNE SYSTEM; IMMUNE SYSTEM
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	34.81 Å
回转半径 Rg (电子) rg_electron	34.22 Å
零角强度 I(0) i0	149405000.00
分子量 molecular_weight	94653.0 kDa
排除体积 excluded_volume	116660 Å³
包络体积 envelope_volume	152200 Å³
水化壳体积 shell_volume	37746 Å³
包络直径 envelope_diameter	111.6 Å
壳层 Rg shell_rg	40.04 Å
包络 Rg envelope_rg	33.83 Å
形状 Rg shape_rg	34.21 Å
总 Rg total_rg	34.66 Å
总原子数 total_atoms	6613
残基数 n_residues	848
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	110.6 Å
Rg (实空间) rg_real	34.78 Å
Rg 误差 (实空间) rg_real_error	0.86 Å
I(0) (实空间) i0_real	1.4940e+08
I(0) 误差 (实空间) i0_real_error	2.5450e+06
Rg (倒空间) rg_reciprocal	34.80 Å
I(0) (倒空间) i0_reciprocal	149400000.0000
解质量估计 total_estimate	0.7210
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	41.8 Å
偏度 Skewness skewness	0.198
峰度 Kurtosis kurtosis	-0.705
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	17550000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 0.186; Positv: 1.000; Valcen: 0.981; Smooth: 0.948

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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	FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, LIGHT CHAIN
分子量 formula_weight	23355.8 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,L
原子数 atom_count	6967

DIELTQSPAIMAASPGEKVTITCSATSGVNYMHWFQQKPGTSPKLWIYSTSNLASAVPARFSGSGSGTSYSLTISRMEAEDAATYYCQQRSTYPFTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	MOUSE
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	MUS MUSCULUS

Entity 2 polymer

描述 description	FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, HEAVY CHAIN
分子量 formula_weight	24501.4 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,H

EVKLQESGGGLVQPGHSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGLIRNKANGYTKEYSASVKGRFTISRDNSQSILYLQMNALRAEDSATYYCVRDKGSYGNYEAWFAYWGQGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRD

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	MOUSE
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	MUS MUSCULUS

Entity 3 non-polymer

描述 description	IODIDE ION
分子量 formula_weight	126.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 4 non-polymer

描述 description	N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE
分子量 formula_weight	320.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	354

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2bmka1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.0 — automated matches

结构域编号 domain_id	d2bmka2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d2bmkb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d2bmkb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d2bmkh1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d2bmkh2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d2bmkl1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.0 — automated matches

结构域编号 domain_id	d2bmkl2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (8 domains)

结构域编号 domain_id	2bmkA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2bmkA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2bmkB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2bmkB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2bmkH01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2bmkH02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2bmkL01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2bmkL02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

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7. 引用文献 (2)

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晶胞边长 a length_a	63.152 Å
晶胞边长 b length_b	81.152 Å
晶胞边长 c length_c	79.331 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.35 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.2097
R_work r_work	0.2097
R_free r_free	0.2725

fit	/app/data/saxs_computation/bm/2bmk/2bmk.fit
pddf	/app/data/pr_computation/bm/2bmk/2bmk.pr.out
profile	/app/data/saxs_computation/bm/2bmk/2bmk.dat

Fab fragment of PLP-dependent catalytic antibody 15A9 in complex with phosphopyridoxyl-D-alanine

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

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

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

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

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)