SAXSdb — 2fta

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2fta
沉积日期 deposition_date	2006-01-24
结构标题 title	;Structure of Cu(II)azurin with the metal-binding loop sequence "CTFPGHSALM" replaced with "CTPHPFM" ;
关键词 keywords	Blue copper-binding protein, greek-key beta-barrel, ELECTRON TRANSPORT; ELECTRON TRANSPORT
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	37.49 Å
回转半径 Rg (电子) rg_electron	38.40 Å
零角强度 I(0) i0	51374900.00
分子量 molecular_weight	55161.0 kDa
排除体积 excluded_volume	68351 Å³
包络体积 envelope_volume	103510 Å³
水化壳体积 shell_volume	27250 Å³
包络直径 envelope_diameter	127.5 Å
壳层 Rg shell_rg	35.93 Å
包络 Rg envelope_rg	37.78 Å
形状 Rg shape_rg	38.39 Å
总 Rg total_rg	38.25 Å
总原子数 total_atoms	3838
残基数 n_residues	491
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	121.8 Å
Rg (实空间) rg_real	38.23 Å
Rg 误差 (实空间) rg_real_error	1.41 Å
I(0) (实空间) i0_real	5.1370e+07
I(0) 误差 (实空间) i0_real_error	9.2770e+05
Rg (倒空间) rg_reciprocal	37.78 Å
I(0) (倒空间) i0_reciprocal	51350000.0000
解质量估计 total_estimate	0.6952
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	4
主峰位置 r_peak_primary	20.3 Å
偏度 Skewness skewness	0.607
峰度 Kurtosis kurtosis	-0.288
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1817000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.516; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.485; Smooth: 0.000

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (6)

Entity 1 polymer

描述 description	Azurin
分子量 formula_weight	13730.5 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	4285

AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTPHPFMKGTLTLK

来源 Source

来源生物 organism	Pseudomonas aeruginosa
NCBI 分类编号 ncbi_taxonomy_id	287
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	COPPER (II) ION
分子量 formula_weight	63.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	NONAETHYLENE GLYCOL
分子量 formula_weight	414.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	ETHANOL
分子量 formula_weight	46.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 5 non-polymer

描述 description	DI(HYDROXYETHYL)ETHER
分子量 formula_weight	106.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 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	447

▼

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2ftaa_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.6 — Cupredoxin-like
超家族 Superfamily superfamily	b.6.1 — Cupredoxins
家族 Family family	b.6.1.1 — Plastocyanin/azurin-like

结构域编号 domain_id	d2ftab_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.6 — Cupredoxin-like
超家族 Superfamily superfamily	b.6.1 — Cupredoxins
家族 Family family	b.6.1.1 — Plastocyanin/azurin-like

结构域编号 domain_id	d2ftac_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.6 — Cupredoxin-like
超家族 Superfamily superfamily	b.6.1 — Cupredoxins
家族 Family family	b.6.1.1 — Plastocyanin/azurin-like

结构域编号 domain_id	d2ftad_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.6 — Cupredoxin-like
超家族 Superfamily superfamily	b.6.1 — Cupredoxins
家族 Family family	b.6.1.1 — Plastocyanin/azurin-like

CATH v4.4 (4 domains)

结构域编号 domain_id	2ftaA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

结构域编号 domain_id	2ftaB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

结构域编号 domain_id	2ftaC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

结构域编号 domain_id	2ftaD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

▶

7. 引用文献 (4)

▶

晶胞边长 a length_a	36.840 Å
晶胞边长 b length_b	97.630 Å
晶胞边长 c length_c	61.120 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.31 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	1.610 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.2330
R_free r_free	0.2690

fit	/app/data/saxs_computation/ft/2fta/2fta.fit
pddf	/app/data/pr_computation/ft/2fta/2fta.pr.out
profile	/app/data/saxs_computation/ft/2fta/2fta.dat

;Structure of Cu(II)azurin with the metal-binding loop sequence "CTFPGHSALM" replaced with "CTPHPFM" ;

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 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (4)

8. 文件与曲线 (10)

Files (7)

Curves (3)