1q4q

Crystal structure of a DIAP1-Dronc complex

Method: X-RAY DIFFRACTION D_max: 132.9 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	1q4q
沉积日期 deposition_date	2003-08-04
结构标题 title	Crystal structure of a DIAP1-Dronc complex
关键词 keywords	caspase, IAP, ubiquitination, apoptosis, APOPTOSIS INHIBITOR; APOPTOSIS INHIBITOR
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	42.20 Å
回转半径 Rg (电子) rg_electron	42.82 Å
零角强度 I(0) i0	219844000.00
分子量 molecular_weight	122200.0 kDa
排除体积 excluded_volume	152910 Å³
包络体积 envelope_volume	207590 Å³
水化壳体积 shell_volume	43433 Å³
包络直径 envelope_diameter	143.0 Å
壳层 Rg shell_rg	43.53 Å
包络 Rg envelope_rg	42.53 Å
形状 Rg shape_rg	42.80 Å
总 Rg total_rg	42.93 Å
总原子数 total_atoms	8609
残基数 n_residues	1043
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	132.9 Å
Rg (实空间) rg_real	42.62 Å
Rg 误差 (实空间) rg_real_error	1.26 Å
I(0) (实空间) i0_real	2.1980e+08
I(0) 误差 (实空间) i0_real_error	3.8980e+06
Rg (倒空间) rg_reciprocal	42.20 Å
I(0) (倒空间) i0_reciprocal	219700000.0000
解质量估计 total_estimate	0.8042
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	35.9 Å
偏度 Skewness skewness	0.523
峰度 Kurtosis kurtosis	-0.473
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	11710000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.875; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.826; Smooth: 0.003

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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 (4)

Entity 1 polymer

描述 description	Apoptosis 1 inhibitor
分子量 formula_weight	14078.7 kDa
来源方法 src_method	man
拷贝数 entity_count	10

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J
原子数 atom_count	9166

DVQPETCRPSAASGNYFPQYPEYAIETARLRTFEAWPRNLKQKPHQLAEAGFFYTGVGDRVRCFSCGGGLMDWNDNDEPWEQHALWLSQCRFVKLMKGQLYIDTVAAKPVLAEEKEESTSIGGD

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	fruit fly
NCBI 分类编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Nedd2-like caspase CG8091-PA
分子量 formula_weight	1474.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

聚合体 Polymer

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

SRPPFISLNERR

Entity 3 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	10

Entity 4 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	557

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6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d1q4qa_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.52 — Inhibitor of apoptosis (IAP) repeat
超家族 Superfamily superfamily	g.52.1 — Inhibitor of apoptosis (IAP) repeat
家族 Family family	g.52.1.1 — Inhibitor of apoptosis (IAP) repeat

结构域编号 domain_id	d1q4qb_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.52 — Inhibitor of apoptosis (IAP) repeat
超家族 Superfamily superfamily	g.52.1 — Inhibitor of apoptosis (IAP) repeat
家族 Family family	g.52.1.1 — Inhibitor of apoptosis (IAP) repeat

结构域编号 domain_id	d1q4qc_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.52 — Inhibitor of apoptosis (IAP) repeat
超家族 Superfamily superfamily	g.52.1 — Inhibitor of apoptosis (IAP) repeat
家族 Family family	g.52.1.1 — Inhibitor of apoptosis (IAP) repeat

结构域编号 domain_id	d1q4qd_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.52 — Inhibitor of apoptosis (IAP) repeat
超家族 Superfamily superfamily	g.52.1 — Inhibitor of apoptosis (IAP) repeat
家族 Family family	g.52.1.1 — Inhibitor of apoptosis (IAP) repeat

结构域编号 domain_id	d1q4qe_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.52 — Inhibitor of apoptosis (IAP) repeat
超家族 Superfamily superfamily	g.52.1 — Inhibitor of apoptosis (IAP) repeat
家族 Family family	g.52.1.1 — Inhibitor of apoptosis (IAP) repeat

结构域编号 domain_id	d1q4qf_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.52 — Inhibitor of apoptosis (IAP) repeat
超家族 Superfamily superfamily	g.52.1 — Inhibitor of apoptosis (IAP) repeat
家族 Family family	g.52.1.1 — Inhibitor of apoptosis (IAP) repeat

结构域编号 domain_id	d1q4qg_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.52 — Inhibitor of apoptosis (IAP) repeat
超家族 Superfamily superfamily	g.52.1 — Inhibitor of apoptosis (IAP) repeat
家族 Family family	g.52.1.1 — Inhibitor of apoptosis (IAP) repeat

结构域编号 domain_id	d1q4qh_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.52 — Inhibitor of apoptosis (IAP) repeat
超家族 Superfamily superfamily	g.52.1 — Inhibitor of apoptosis (IAP) repeat
家族 Family family	g.52.1.1 — Inhibitor of apoptosis (IAP) repeat

结构域编号 domain_id	d1q4qi_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.52 — Inhibitor of apoptosis (IAP) repeat
超家族 Superfamily superfamily	g.52.1 — Inhibitor of apoptosis (IAP) repeat
家族 Family family	g.52.1.1 — Inhibitor of apoptosis (IAP) repeat

结构域编号 domain_id	d1q4qj_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.52 — Inhibitor of apoptosis (IAP) repeat
超家族 Superfamily superfamily	g.52.1 — Inhibitor of apoptosis (IAP) repeat
家族 Family family	g.52.1.1 — Inhibitor of apoptosis (IAP) repeat

CATH v4.4 (10 domains)

结构域编号 domain_id	1q4qA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
同源超家族 H-superfamily homologous superfamily	10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A

结构域编号 domain_id	1q4qB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
同源超家族 H-superfamily homologous superfamily	10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A

结构域编号 domain_id	1q4qC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
同源超家族 H-superfamily homologous superfamily	10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A

结构域编号 domain_id	1q4qD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
同源超家族 H-superfamily homologous superfamily	10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A

结构域编号 domain_id	1q4qE00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
同源超家族 H-superfamily homologous superfamily	10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A

结构域编号 domain_id	1q4qF00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
同源超家族 H-superfamily homologous superfamily	10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A

结构域编号 domain_id	1q4qG00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
同源超家族 H-superfamily homologous superfamily	10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A

结构域编号 domain_id	1q4qH00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
同源超家族 H-superfamily homologous superfamily	10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A

结构域编号 domain_id	1q4qI00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
同源超家族 H-superfamily homologous superfamily	10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A

结构域编号 domain_id	1q4qJ00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
同源超家族 H-superfamily homologous superfamily	10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A

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7. 引用文献 (1)

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晶胞边长 a length_a	128.900 Å
晶胞边长 b length_b	128.900 Å
晶胞边长 c length_c	183.695 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	60

空间群 space_group	P 65
空间群编号 int_tables_number	170
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2030
R_work r_work	0.1990
R_free r_free	0.2460

fit	/app/data/saxs_computation/q4/1q4q/1q4q.fit
pddf	/app/data/pr_computation/q4/1q4q/1q4q.pr.out
profile	/app/data/saxs_computation/q4/1q4q/1q4q.dat

Crystal structure of a DIAP1-Dronc complex

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)