SAXSdb — 1y64

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1y64
沉积日期 deposition_date	2004-12-03
结构标题 title	Bni1p Formin Homology 2 Domain complexed with ATP-actin
关键词 keywords	FH2 ACTIN CYTOSKELETON, COILED COIL, ACTIN, TETRAMETHYLRHODAMINE-5-MALEIMIDE, ATP-STATE, 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	33.81 Å
回转半径 Rg (电子) rg_electron	33.43 Å
零角强度 I(0) i0	120331000.00
分子量 molecular_weight	87654.0 kDa
排除体积 excluded_volume	109960 Å³
包络体积 envelope_volume	153060 Å³
水化壳体积 shell_volume	39124 Å³
包络直径 envelope_diameter	124.3 Å
壳层 Rg shell_rg	38.77 Å
包络 Rg envelope_rg	34.38 Å
形状 Rg shape_rg	33.48 Å
总 Rg total_rg	33.72 Å
总原子数 total_atoms	6162
残基数 n_residues	767
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	113.7 Å
Rg (实空间) rg_real	33.90 Å
Rg 误差 (实空间) rg_real_error	1.02 Å
I(0) (实空间) i0_real	1.2030e+08
I(0) 误差 (实空间) i0_real_error	2.0340e+06
Rg (倒空间) rg_reciprocal	33.85 Å
I(0) (倒空间) i0_reciprocal	120300000.0000
解质量估计 total_estimate	0.8681
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	38.7 Å
偏度 Skewness skewness	0.416
峰度 Kurtosis kurtosis	-0.233
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15490000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.929; Smooth: 0.718

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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	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	6162

DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF

Entity 2 polymer

描述 description	BNI1 protein
分子量 formula_weight	50922.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

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

MPASQIKSAVTSPLLPQSPSLFEKYPRPHKKLKQLHWEKLDCTDNSIWGTGKAEKFADDLYEKGVLADLEKAFAAREIKSLASKRKEDLQKITFLSRDISQQFGINLHMYSSLSVADLVKKILNCDRDFLQTPSVVEFLSKSEIIEVSVNLARNYAPYSTDWEGVRNLEDAKPPEKDPNDLQRADQIYLQLMVNLESYWGSRMRALTVVTSYEREYNELLAKLRKVDKAVSALQESDNLRNVFNVILAVGNFMNDTSKQAQGFKLSTLQRLTFIKDTTNSMTFLNYVEKIVRLNYPSFNDFLSELEPVLDVVKVSIEQLVNDCKDFSQSIVNVERSVEIGNLSDSSKFHPLDKVLIKTLPVLPEARKKGDLLEDEVKLTIMEFESLMHTYGEDSGDKFAKISFFKKFADFINEYKKAQAQNLAAEEEERLYIKHKKIVEEQQK

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 3 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	1

Entity 4 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

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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	d1y64a1
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.55.1.0 — automated matches

结构域编号 domain_id	d1y64a2
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	d1y64b_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.207 — Formin homology 2 domain (FH2 domain)
超家族 Superfamily superfamily	a.207.1 — Formin homology 2 domain (FH2 domain)
家族 Family family	a.207.1.1 — Formin homology 2 domain (FH2 domain)

CATH v4.4 (5 domains)

结构域编号 domain_id	1y64A01
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	1y64A02
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	1y64A03
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	1y64B01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	30 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1y64B03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	2220 — Formin, FH2 domain

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7. 引用文献 (3)

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晶胞边长 a length_a	231.997 Å
晶胞边长 b length_b	56.229 Å
晶胞边长 c length_c	100.945 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	107.70 °
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	3.050 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.3130
R_work r_work	0.2890
R_free r_free	0.3130

fit	/app/data/saxs_computation/y6/1y64/1y64.fit
pddf	/app/data/pr_computation/y6/1y64/1y64.pr.out
profile	/app/data/saxs_computation/y6/1y64/1y64.dat

Bni1p Formin Homology 2 Domain complexed with ATP-actin

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

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (3 domains)

CATH v4.4 (5 domains)

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)