SAXSdb — 1w5a

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1w5a
沉积日期 deposition_date	2004-08-06
结构标题 title	FtsZ dimer, MgGTP soak (M. jannaschii)
关键词 keywords	;CELL DIVISION, CELL DIVISION PROTEIN, CELL-DIVISION PROTEIN, FTSZ, GTP-BINDING, MULTIGENE FAMILY, SEPTATION, TUBULIN, FILAMENT, Z-RING, GTPASE ;; CELL DIVISION
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	29.91 Å
回转半径 Rg (电子) rg_electron	29.49 Å
零角强度 I(0) i0	83093400.00
分子量 molecular_weight	71939.0 kDa
排除体积 excluded_volume	90448 Å³
包络体积 envelope_volume	111710 Å³
水化壳体积 shell_volume	32804 Å³
包络直径 envelope_diameter	112.5 Å
壳层 Rg shell_rg	35.24 Å
包络 Rg envelope_rg	29.77 Å
形状 Rg shape_rg	29.50 Å
总 Rg total_rg	29.99 Å
总原子数 total_atoms	5024
残基数 n_residues	670
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	105.1 Å
Rg (实空间) rg_real	30.09 Å
Rg 误差 (实空间) rg_real_error	1.16 Å
I(0) (实空间) i0_real	8.3090e+07
I(0) 误差 (实空间) i0_real_error	1.3880e+06
Rg (倒空间) rg_reciprocal	30.01 Å
I(0) (倒空间) i0_reciprocal	83090000.0000
解质量估计 total_estimate	0.8438
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	29.8 Å
偏度 Skewness skewness	0.535
峰度 Kurtosis kurtosis	-0.198
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15440000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.710; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.862; Smooth: 0.977

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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	CELL DIVISION PROTEIN FTSZ HOMOLOG 1
分子量 formula_weight	38970.1 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	5271

MKFLKNVLEEGSKLEEFNELELSPEDKELLEYLQQTKAKITVVGCGGAGNNTITRLKMEGIEGAKTVAINTDAQQLIRTKADKKILIGKKLTRGLGAGGNPKIGEEAAKESAEEIKAAIQDSDMVFITCGLGGGTGTGSAPVVAEISKKIGALTVAVVTLPFVMEGKVRMKNAMEGLERLKQHTDTLVVIPNEKLFEIVPNMPLKLAFKVADEVLINAVKGLVELITKDGLINVDFADVKAVMNNGGLAMIGIGESDSEKRAKEAVSMALNSPLLDVDIDGATGALIHVMGPEDLTLEEAREVVATVSSRLDPNATIIWGATIDENLENTVRVLLVITGVQSRIEFTDTGLKRKKLELTGIPKI

来源 Source

来源生物 organism	METHANOCALDOCOCCUS JANNASCHII
NCBI 分类编号 ncbi_taxonomy_id	2190
宿主生物 host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 2 non-polymer

描述 description	GUANOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	523.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	1

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	247

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1w5aa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.32 — Tubulin nucleotide-binding domain-like
超家族 Superfamily superfamily	c.32.1 — Tubulin nucleotide-binding domain-like
家族 Family family	c.32.1.1 — Tubulin, GTPase domain

结构域编号 domain_id	d1w5aa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.2 — Tubulin C-terminal domain-like
家族 Family family	d.79.2.1 — Tubulin, C-terminal domain

结构域编号 domain_id	d1w5ab1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.32 — Tubulin nucleotide-binding domain-like
超家族 Superfamily superfamily	c.32.1 — Tubulin nucleotide-binding domain-like
家族 Family family	c.32.1.1 — Tubulin, GTPase domain

结构域编号 domain_id	d1w5ab2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.2 — Tubulin C-terminal domain-like
家族 Family family	d.79.2.1 — Tubulin, C-terminal domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1w5aA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1440 — Tubulin/FtsZ, GTPase domain

结构域编号 domain_id	1w5aA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	20 — Tubulin/FtsZ, C-terminal domain

结构域编号 domain_id	1w5aB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1440 — Tubulin/FtsZ, GTPase domain

结构域编号 domain_id	1w5aB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	20 — Tubulin/FtsZ, C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	70.436 Å
晶胞边长 b length_b	55.222 Å
晶胞边长 c length_c	88.127 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	91.33 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.2640

fit	/app/data/saxs_computation/w5/1w5a/1w5a.fit
pddf	/app/data/pr_computation/w5/1w5a/1w5a.pr.out
profile	/app/data/saxs_computation/w5/1w5a/1w5a.dat

FtsZ dimer, MgGTP soak (M. jannaschii)

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