SAXSdb — 1fdu

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1fdu
沉积日期 deposition_date	1998-01-14
结构标题 title	HUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 MUTANT H221L COMPLEXED WITH ESTRADIOL AND NADP+
关键词 keywords	DEHYDROGENASE, 17-BETA-HYDROXYSTEROID, MUTANT, ESTRADIOL, NADP; DEHYDROGENASE
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	38.34 Å
回转半径 Rg (电子) rg_electron	37.94 Å
零角强度 I(0) i0	242049000.00
分子量 molecular_weight	127190.0 kDa
排除体积 excluded_volume	159510 Å³
包络体积 envelope_volume	195500 Å³
水化壳体积 shell_volume	43062 Å³
包络直径 envelope_diameter	124.2 Å
壳层 Rg shell_rg	43.75 Å
包络 Rg envelope_rg	37.50 Å
形状 Rg shape_rg	37.96 Å
总 Rg total_rg	38.22 Å
总原子数 total_atoms	8916
残基数 n_residues	1127
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	122.6 Å
Rg (实空间) rg_real	38.42 Å
Rg 误差 (实空间) rg_real_error	0.87 Å
I(0) (实空间) i0_real	2.4200e+08
I(0) 误差 (实空间) i0_real_error	4.1460e+06
Rg (倒空间) rg_reciprocal	38.38 Å
I(0) (倒空间) i0_reciprocal	242000000.0000
解质量估计 total_estimate	0.8125
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	32.9 Å
偏度 Skewness skewness	0.241
峰度 Kurtosis kurtosis	-0.822
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	62200000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.928; Smooth: 0.000

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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 (5)

Entity 1 polymer

描述 description	17-BETA-HYDROXYSTEROID DEHYDROGENASE
分子量 formula_weight	34949.0 kDa
EC 编号 ec_number	1.1.1.62
突变 mutation	H221L
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	9114

ARTVVLITGCSSGIGLHLAVRLASDPSQSFKVYATLRDLKTQGRLWEAARALACPPGSLETLQLDVRDSKSVAAARERVTEGRVDVLVCNAGLGLLGPLEALGEDAVASVLDVNVVGTVRMLQAFLPDMKRRGSGRVLVTGSVGGLMGLPFNDVYCASKFALEGLCESLAVLLLPFGVHLSLIECGPVHTAFMEKVLGSPEEVLDRTDIHTFHRFYQYLALSKQVFREAAQNPEEVAEVFLTALRAPKPTLRYFTTERFLPLLRMRLDDPSGSNYVTAMHREVFGDVPAKAEAGAEAGGGRGPGAEDEAGRSAVGDPELGDPPAAPQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	ESTRADIOL
分子量 formula_weight	272.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
分子量 formula_weight	743.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 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	198

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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	d1fdua_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

结构域编号 domain_id	d1fdub_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

结构域编号 domain_id	d1fduc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

结构域编号 domain_id	d1fdud_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

CATH v4.4 (4 domains)

结构域编号 domain_id	1fduA00
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1fduB00
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1fduC00
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1fduD00
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	720 — NAD(P)-binding Rossmann-like Domain

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7. 引用文献 (4)

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晶胞边长 a length_a	115.800 Å
晶胞边长 b length_b	78.780 Å
晶胞边长 c length_c	121.190 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	92.91 °
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	2.700 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	—
R_work r_work	0.2200
R_free r_free	0.2950

fit	/app/data/saxs_computation/fd/1fdu/1fdu.fit
pddf	/app/data/pr_computation/fd/1fdu/1fdu.pr.out
profile	/app/data/saxs_computation/fd/1fdu/1fdu.dat

HUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 MUTANT H221L COMPLEXED WITH ESTRADIOL AND NADP+

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