1lvc

;Crystal structure of the adenylyl cyclase domain of anthrax edema factor (EF) in complex with calmodulin and 2' deoxy, 3' anthraniloyl ATP ;

Method: X-RAY DIFFRACTION D_max: 125.1 Å Quality: GOOD

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	1lvc
沉积日期 deposition_date	2002-05-28
结构标题 title	;Crystal structure of the adenylyl cyclase domain of anthrax edema factor (EF) in complex with calmodulin and 2' deoxy, 3' anthraniloyl ATP ;
关键词 keywords	helical domain, protein-protein complex, LYASE; LYASE
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	41.20 Å
回转半径 Rg (电子) rg_electron	40.66 Å
零角强度 I(0) i0	702908000.00
分子量 molecular_weight	217680.0 kDa
排除体积 excluded_volume	272440 Å³
包络体积 envelope_volume	389800 Å³
水化壳体积 shell_volume	76948 Å³
包络直径 envelope_diameter	128.6 Å
壳层 Rg shell_rg	49.07 Å
包络 Rg envelope_rg	39.36 Å
形状 Rg shape_rg	40.66 Å
总 Rg total_rg	41.10 Å
总原子数 total_atoms	15302
残基数 n_residues	1882
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	125.1 Å
Rg (实空间) rg_real	40.95 Å
Rg 误差 (实空间) rg_real_error	0.67 Å
I(0) (实空间) i0_real	7.0290e+08
I(0) 误差 (实空间) i0_real_error	1.0490e+07
Rg (倒空间) rg_reciprocal	41.20 Å
I(0) (倒空间) i0_reciprocal	703100000.0000
解质量估计 total_estimate	0.8967
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	56.0 Å
偏度 Skewness skewness	0.022
峰度 Kurtosis kurtosis	-0.554
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	70620000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.890

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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	calmodulin-sensitive adenylate cyclase
分子量 formula_weight	58810.6 kDa
EC 编号 ec_number	4.6.1.1
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	15302

DRIDVLKGEKALKASGLVPEHADAFKKIARELNTYILFRPVNKLATNLIKSGVATKGLNVHGKSSDWGPVAGYIPFDQDLSKKHGQQLAVEKGNLENKKSITEHEGEIGKIPLKLDHLRIEELKENGIILKGKKEIDNGKKYYLLESNNQVYEFRISDENNEVQYKTKEGKITVLGEKFNWRNIEVMAKNVEGVLKPLTADYDLFALAPSLTEIKKQIPQKEWDKVVNTPNSLEKQKGVTNLLIKYGIERKPDSTKGTLSNWQKQMLDRLNEAVKYTGYTGGDVVNHGTEQDNEEFPEKDNEIFIINPEGEFILTKNWEMTGRFIEKNITGKDYLYYFNRSYNKIAPGNKAYIEWTDPITKAKINTIPTSAEFIKNLSSIRRSSNVGVYKDSGDKDEFAKKESVKKIAGYLSDYYNSANHIFSQEKKRKISIFRGIQAYNEIENVLKSKQIAPEYKNYFQYLKERITNQVQLLLTHQKSNIEFKLLYKQLNFTENETDNFEVFQKIIDEK

来源 Source

来源生物 organism	Bacillus anthracis
NCBI 分类编号 ncbi_taxonomy_id	1392
宿主生物 host_organism	Escherichia coli BL21

Entity 2 polymer

描述 description	calmodulin
分子量 formula_weight	16852.5 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D,E,F

MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21

Entity 3 non-polymer

描述 description	YTTERBIUM (III) ION
分子量 formula_weight	173.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 4 non-polymer

描述 description	3'ANTHRANILOYL-2'-DEOXY-ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	610.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	6

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1lvca_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.41 — Adenylylcyclase toxin (the edema factor)
超家族 Superfamily superfamily	e.41.1 — Adenylylcyclase toxin (the edema factor)
家族 Family family	e.41.1.1 — Adenylylcyclase toxin (the edema factor)

结构域编号 domain_id	d1lvcb_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.41 — Adenylylcyclase toxin (the edema factor)
超家族 Superfamily superfamily	e.41.1 — Adenylylcyclase toxin (the edema factor)
家族 Family family	e.41.1.1 — Adenylylcyclase toxin (the edema factor)

结构域编号 domain_id	d1lvcc_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.41 — Adenylylcyclase toxin (the edema factor)
超家族 Superfamily superfamily	e.41.1 — Adenylylcyclase toxin (the edema factor)
家族 Family family	e.41.1.1 — Adenylylcyclase toxin (the edema factor)

结构域编号 domain_id	d1lvcd_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.39 — EF Hand-like
超家族 Superfamily superfamily	a.39.1 — EF-hand
家族 Family family	a.39.1.5 — Calmodulin-like

结构域编号 domain_id	d1lvce_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.39 — EF Hand-like
超家族 Superfamily superfamily	a.39.1 — EF-hand
家族 Family family	a.39.1.5 — Calmodulin-like

结构域编号 domain_id	d1lvcf_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.39 — EF Hand-like
超家族 Superfamily superfamily	a.39.1 — EF-hand
家族 Family family	a.39.1.5 — Calmodulin-like

CATH v4.4 (12 domains)

结构域编号 domain_id	1lvcA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1760 — Adenylylcyclase toxin fold
同源超家族 H-superfamily homologous superfamily	10 — Anthrax toxin, edema factor, central domain

结构域编号 domain_id	1lvcA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
同源超家族 H-superfamily homologous superfamily	60 —

结构域编号 domain_id	1lvcB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1760 — Adenylylcyclase toxin fold
同源超家族 H-superfamily homologous superfamily	10 — Anthrax toxin, edema factor, central domain

结构域编号 domain_id	1lvcB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
同源超家族 H-superfamily homologous superfamily	60 —

结构域编号 domain_id	1lvcC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1760 — Adenylylcyclase toxin fold
同源超家族 H-superfamily homologous superfamily	10 — Anthrax toxin, edema factor, central domain

结构域编号 domain_id	1lvcC03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
同源超家族 H-superfamily homologous superfamily	60 —

结构域编号 domain_id	1lvcD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	238 — Recoverin; domain 1
同源超家族 H-superfamily homologous superfamily	10 — EF-hand

结构域编号 domain_id	1lvcD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	238 — Recoverin; domain 1
同源超家族 H-superfamily homologous superfamily	10 — EF-hand

结构域编号 domain_id	1lvcE01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	238 — Recoverin; domain 1
同源超家族 H-superfamily homologous superfamily	10 — EF-hand

结构域编号 domain_id	1lvcE02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	238 — Recoverin; domain 1
同源超家族 H-superfamily homologous superfamily	10 — EF-hand

结构域编号 domain_id	1lvcF01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	238 — Recoverin; domain 1
同源超家族 H-superfamily homologous superfamily	10 — EF-hand

结构域编号 domain_id	1lvcF02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	238 — Recoverin; domain 1
同源超家族 H-superfamily homologous superfamily	10 — EF-hand

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7. 引用文献 (2)

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晶胞边长 a length_a	116.924 Å
晶胞边长 b length_b	167.918 Å
晶胞边长 c length_c	341.743 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	24

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	3.600 Å
最低分辨率 resolution_low	29.960 Å
R 因子 r_factor	0.2810
R_work r_work	0.2810
R_free r_free	0.3070

fit	/app/data/saxs_computation/lv/1lvc/1lvc.fit
pddf	/app/data/pr_computation/lv/1lvc/1lvc.pr.out
profile	/app/data/saxs_computation/lv/1lvc/1lvc.dat

;Crystal structure of the adenylyl cyclase domain of anthrax edema factor (EF) in complex with calmodulin and 2' deoxy, 3' anthraniloyl ATP ;

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 non-polymer

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)