2a3z

Ternary complex of the WH2 domain of WASP with Actin-DNAse I

Method: X-RAY DIFFRACTION D_max: 99.7 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	2a3z
沉积日期 deposition_date	2005-06-27
结构标题 title	Ternary complex of the WH2 domain of WASP with Actin-DNAse I
关键词 keywords	WASP, WH2, actin, DNAse I, arp2/3, STRUCTURAL PROTEIN; STRUCTURAL 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	30.68 Å
回转半径 Rg (电子) rg_electron	30.24 Å
零角强度 I(0) i0	85482800.00
分子量 molecular_weight	72498.0 kDa
排除体积 excluded_volume	90403 Å³
包络体积 envelope_volume	110660 Å³
水化壳体积 shell_volume	31213 Å³
包络直径 envelope_diameter	101.9 Å
壳层 Rg shell_rg	36.56 Å
包络 Rg envelope_rg	29.93 Å
形状 Rg shape_rg	30.23 Å
总 Rg total_rg	30.83 Å
总原子数 total_atoms	5086
残基数 n_residues	637
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	99.7 Å
Rg (实空间) rg_real	30.77 Å
Rg 误差 (实空间) rg_real_error	0.60 Å
I(0) (实空间) i0_real	8.5480e+07
I(0) 误差 (实空间) i0_real_error	1.1890e+06
Rg (倒空间) rg_reciprocal	30.74 Å
I(0) (倒空间) i0_reciprocal	85480000.0000
解质量估计 total_estimate	0.6707
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	28.8 Å
偏度 Skewness skewness	0.352
峰度 Kurtosis kurtosis	-0.588
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	16760000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 0.077; Positv: 1.000; Valcen: 0.912; Smooth: 0.897

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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 (10)

Entity 1 polymer

描述 description	Actin, alpha skeletal muscle
分子量 formula_weight	41875.6 kDa
来源方法 src_method	nat
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	5584

DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF

Entity 2 polymer

描述 description	Deoxyribonuclease-1
分子量 formula_weight	29092.6 kDa
EC 编号 ec_number	3.1.21.1
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

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

LKIAAFNIRTFGETKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAVGKLLDYLNQDDPNTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDGCESCGNDSFSREPAVVKFSSHSTKVKEFAIVALHSAPSDAVAEINSLYDVYLDVQQKWHLNDVMLMGDFNADCSYVTSSQWSSIRLRTSSTFQWLIPDSADTTATSTNCAYDRIVVAGSLLQSSVVPGSAAPFDFQAAYGLSNEMALAISDHYPVEVTLT

Entity 3 polymer

描述 description	Wiskott-Aldrich syndrome protein
分子量 formula_weight	3019.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C

GRGALLDQIRQGIQLNKTPGAPESSALQP

Entity 4 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 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	2

Entity 6 non-polymer

描述 description	ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 8 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	1

Entity 9 non-polymer

描述 description	FORMIC ACID
分子量 formula_weight	46.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 10 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	395

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d2a3za1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.1 — Actin/HSP70

结构域编号 domain_id	d2a3za2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.1 — Actin/HSP70

结构域编号 domain_id	d2a3zb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.151 — DNase I-like
超家族 Superfamily superfamily	d.151.1 — DNase I-like
家族 Family family	d.151.1.1 — DNase I-like

CATH v4.4 (5 domains)

结构域编号 domain_id	2a3zA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	2a3zA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	36 — Actin; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	70 — Actin; Chain A, domain 2

结构域编号 domain_id	2a3zA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	2a3zA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	640 — Actin; Chain A, domain 4
同源超家族 H-superfamily homologous superfamily	10 — ATPase, substrate binding domain, subdomain 4

结构域编号 domain_id	2a3zB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	10 — Deoxyribonuclease I; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Endonuclease/exonuclease/phosphatase

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7. 引用文献 (1)

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晶胞边长 a length_a	153.270 Å
晶胞边长 b length_b	41.798 Å
晶胞边长 c length_c	119.418 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	108.68 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	2.078 Å
最低分辨率 resolution_low	40.100 Å
R 因子 r_factor	0.1591
R_work r_work	0.1533
R_free r_free	0.2103

fit	/app/data/saxs_computation/a3/2a3z/2a3z.fit
pddf	/app/data/pr_computation/a3/2a3z/2a3z.pr.out
profile	/app/data/saxs_computation/a3/2a3z/2a3z.dat

Ternary complex of the WH2 domain of WASP with Actin-DNAse I

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 (10)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 branched

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (3 domains)

CATH v4.4 (5 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)