SAXSdb — 1w5b

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1w5b
沉积日期 deposition_date	2004-08-06
结构标题 title	FtsZ dimer, GTP 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	29.89 Å
回转半径 Rg (电子) rg_electron	29.48 Å
零角强度 I(0) i0	82892200.00
分子量 molecular_weight	71915.0 kDa
排除体积 excluded_volume	90426 Å³
包络体积 envelope_volume	111390 Å³
水化壳体积 shell_volume	32726 Å³
包络直径 envelope_diameter	112.5 Å
壳层 Rg shell_rg	35.21 Å
包络 Rg envelope_rg	29.80 Å
形状 Rg shape_rg	29.49 Å
总 Rg total_rg	29.99 Å
总原子数 total_atoms	5023
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	30.08 Å
Rg 误差 (实空间) rg_real_error	1.08 Å
I(0) (实空间) i0_real	8.2890e+07
I(0) 误差 (实空间) i0_real_error	1.3580e+06
Rg (倒空间) rg_reciprocal	30.00 Å
I(0) (倒空间) i0_reciprocal	82890000.0000
解质量估计 total_estimate	0.8440
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	29.7 Å
偏度 Skewness skewness	0.536
峰度 Kurtosis kurtosis	-0.196
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	15340000.0000
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: 0.709; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.862; Smooth: 0.982

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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 (3)

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	5270

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 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	d1w5ba1
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	d1w5ba2
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	d1w5bb1
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	d1w5bb2
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	1w5bA01
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	1w5bA02
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	1w5bB01
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	1w5bB02
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	70.303 Å
晶胞边长 b length_b	55.203 Å
晶胞边长 c length_c	88.129 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.97 °
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	2.200 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2090
R_work r_work	0.2090
R_free r_free	0.2590

fit	/app/data/saxs_computation/w5/1w5b/1w5b.fit
pddf	/app/data/pr_computation/w5/1w5b/1w5b.pr.out
profile	/app/data/saxs_computation/w5/1w5b/1w5b.dat

FtsZ dimer, GTP 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