1xfv

;Crystal structure of anthrax edema factor (EF) in complex with calmodulin and 3' deoxy-ATP ;

Method: X-RAY DIFFRACTION D_max: 250.1 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	1xfv
沉积日期 deposition_date	2004-09-15
结构标题 title	;Crystal structure of anthrax edema factor (EF) in complex with calmodulin and 3' deoxy-ATP ;
关键词 keywords	protein-protein interactions, LYASE-METAL BINDING PROTEIN COMPLEX; LYASE/METAL BINDING PROTEIN
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	89.21 Å
回转半径 Rg (电子) rg_electron	88.73 Å
零角强度 I(0) i0	5047320000.00
分子量 molecular_weight	611000.0 kDa
排除体积 excluded_volume	766640 Å³
包络体积 envelope_volume	1624600 Å³
水化壳体积 shell_volume	153160 Å³
包络直径 envelope_diameter	258.6 Å
壳层 Rg shell_rg	93.78 Å
包络 Rg envelope_rg	80.80 Å
形状 Rg shape_rg	88.73 Å
总 Rg total_rg	88.77 Å
总原子数 total_atoms	43038
残基数 n_residues	5286
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	250.1 Å
Rg (实空间) rg_real	89.00 Å
Rg 误差 (实空间) rg_real_error	1.15 Å
I(0) (实空间) i0_real	5.0470e+09
I(0) 误差 (实空间) i0_real_error	1.0520e+08
Rg (倒空间) rg_reciprocal	90.17 Å
I(0) (倒空间) i0_reciprocal	5062000000.0000
解质量估计 total_estimate	0.8442
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	147.1 Å
偏度 Skewness skewness	-0.050
峰度 Kurtosis kurtosis	-0.741
角度范围 angular_range	— – 0.0850 Å⁻¹
当前正则化参数 α current_alpha	0.1166
最高正则化参数 α highest_alpha	184100000.0000
实空间数据点数 n_real_points	18
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.992; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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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 (6)

Entity 1 polymer

描述 description	Calmodulin-sensitive adenylate cyclase
分子量 formula_weight	90128.9 kDa
EC 编号 ec_number	4.6.1.1
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	43044

MHHHHHHAAAMNEHYTESDIKRNHKTEKNKTEKEKFKDSINNLVKTEFTNETLDKIQQTQDLLKKIPKDVLEIYSELGGEIYFTDIDLVEHKELQDLSEEEKNSMNSRGEKVPFASRFVFEKKRETPKLIINIKDYAINSEQSKEVYYEIGKGISLDIISKDKSLDPEFLNLIKSLSDDSDSSDLLFSQKFKEKLELNNKSIDINFIKENLTEFQHAFSLAFSYYFAPDHRTVLELYAPDMFEYMNKLEKGGFEKISESLKKEGVEKDRIDVLKGEKALKASGLVPEHADAFKKIARELNTYILFRPVNKLATNLIKSGVATKGLNVHGKSSDWGPVAGYIPFDQDLSKKHGQQLAVEKGNLENKKSITEHEGEIGKIPLKLDHLRIEELKENGIILKGKKEIDNGKKYYLLESNNQVYEFRISDENNEVQYKTKEGKITVLGEKFNWRNIEVMAKNVEGVLKPLTADYDLFALAPSLTEIKKQIPQKEWDKVVNTPNSLEKQKGVTNLLIKYGIERKPDSTKGTLSNWQKQMLDRLNEAVKYTGYTGGDVVNHGTEQDNEEFPEKDNEIFIINPEGEFILTKNWEMTGRFIEKNITGKDYLYYFNRSYNKIAPGNKAYIEWTDPITKAKINTIPTSAEFIKNLSSIRRSSNVGVYKDSGDKDEFAKKESVKKIAGYLSDYYNSANHIFSQEKKRKISIFRGIQAYNEIENVLKSKQIAPEYKNYFQYLKERITNQVQLLLTHQKSNIEFKLLYKQLNFTENETDNFEVFQKIIDEK

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

Entity 2 polymer

描述 description	Calmodulin 2
分子量 formula_weight	16851.6 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	O,P,Q,R,S,T

MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDQMIREADIDGDGQVNYEEFVQMMTAK

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

Entity 3 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 4 non-polymer

描述 description	3'-DEOXYADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	491.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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	18

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	6

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6. 折叠分类 (SCOP + CATH) 36 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1xfvo1
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	d1xfvp1
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	d1xfvq1
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	d1xfvr1
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	d1xfvs1
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	d1xfvt1
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 (30 domains)

结构域编号 domain_id	1xfvA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

结构域编号 domain_id	1xfvA03
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	1xfvA04
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	1xfvB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

结构域编号 domain_id	1xfvB03
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	1xfvB04
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	1xfvC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

结构域编号 domain_id	1xfvC03
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	1xfvC04
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	1xfvD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

结构域编号 domain_id	1xfvD03
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	1xfvD04
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	1xfvE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

结构域编号 domain_id	1xfvE03
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	1xfvE04
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	1xfvF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

结构域编号 domain_id	1xfvF03
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	1xfvF04
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	1xfvO01
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	1xfvO02
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	1xfvP01
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	1xfvP02
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	1xfvQ01
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	1xfvQ02
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	1xfvR01
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	1xfvR02
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	1xfvS01
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	1xfvS02
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	1xfvT01
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	1xfvT02
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 (1)

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晶胞边长 a length_a	184.599 Å
晶胞边长 b length_b	319.285 Å
晶胞边长 c length_c	142.054 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.22 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	3.350 Å
最低分辨率 resolution_low	29.570 Å
R 因子 r_factor	0.2630
R_work r_work	0.2630
R_free r_free	0.2820

;Crystal structure of anthrax edema factor (EF) in complex with calmodulin and 3' deoxy-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 (6)

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

Entity 6 water

6. 折叠分类 (SCOP + CATH) 36 domains

SCOP 2.08 (6 domains)

CATH v4.4 (30 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/xf/1xfv/1xfv.fit
pddf	/app/data/pr_computation/xf/1xfv/1xfv.pr.out
profile	/app/data/saxs_computation/xf/1xfv/1xfv.dat