SAXSdb — 1rfx

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1rfx
沉积日期 deposition_date	2003-11-10
结构标题 title	Crystal Structure of resisitin
关键词 keywords	;HORMONE; GLUCOSE UPTAKE; RESISTIN/FIZZ FAMILY, Structural Genomics, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, HORMONE-GROWTH FACTOR COMPLEX ;; HORMONE/GROWTH FACTOR
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	22.63 Å
回转半径 Rg (电子) rg_electron	22.59 Å
零角强度 I(0) i0	17682500.00
分子量 molecular_weight	29496.0 kDa
排除体积 excluded_volume	35951 Å³
包络体积 envelope_volume	45053 Å³
水化壳体积 shell_volume	18257 Å³
包络直径 envelope_diameter	82.8 Å
壳层 Rg shell_rg	27.18 Å
包络 Rg envelope_rg	23.25 Å
形状 Rg shape_rg	22.58 Å
总 Rg total_rg	23.21 Å
总原子数 total_atoms	2024
残基数 n_residues	267
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	80.8 Å
Rg (实空间) rg_real	22.88 Å
Rg 误差 (实空间) rg_real_error	0.76 Å
I(0) (实空间) i0_real	1.7680e+07
I(0) 误差 (实空间) i0_real_error	2.9680e+05
Rg (倒空间) rg_reciprocal	22.82 Å
I(0) (倒空间) i0_reciprocal	17680000.0000
解质量估计 total_estimate	0.7927
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	22.0 Å
偏度 Skewness skewness	0.643
峰度 Kurtosis kurtosis	-0.158
角度范围 angular_range	— – 0.3500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	3507000.0000
实空间数据点数 n_real_points	67
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.538; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.699; Smooth: 0.987

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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 (6)

Entity 1 polymer

描述 description	Resistin
分子量 formula_weight	10182.8 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	2279

SSMPLCPIDEAIDKKIKQDFNSLFPNAIKNIGLNCWTVSSRGKLASCPEGTAVLSCSCGSACGSWDIREEKVCHCQCARIDWTAARCCKLQVAS

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 2 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	11

Entity 3 non-polymer

描述 description	ACETATE ION
分子量 formula_weight	59.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

Entity 4 non-polymer

描述 description	TRIETHYLENE GLYCOL
分子量 formula_weight	150.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	205

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6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1rfxa_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.77 — Resistin
超家族 Superfamily superfamily	g.77.1 — Resistin
家族 Family family	g.77.1.1 — Resistin

结构域编号 domain_id	d1rfxb_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.77 — Resistin
超家族 Superfamily superfamily	g.77.1 — Resistin
家族 Family family	g.77.1.1 — Resistin

结构域编号 domain_id	d1rfxc_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.77 — Resistin
超家族 Superfamily superfamily	g.77.1 — Resistin
家族 Family family	g.77.1.1 — Resistin

CATH v4.4 (6 domains)

结构域编号 domain_id	1rfxA01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	200 —

结构域编号 domain_id	1rfxA02
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	4230 — Resistin head domain

结构域编号 domain_id	1rfxB01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	200 —

结构域编号 domain_id	1rfxB02
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	4230 — Resistin head domain

结构域编号 domain_id	1rfxC01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	200 —

结构域编号 domain_id	1rfxC02
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	4230 — Resistin head domain

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7. 引用文献 (1)

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晶胞边长 a length_a	44.298 Å
晶胞边长 b length_b	174.670 Å
晶胞边长 c length_c	90.163 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.002 Å
最低分辨率 resolution_low	14.860 Å
R 因子 r_factor	0.1792
R_work r_work	0.1772
R_free r_free	0.2160

fit	/app/data/saxs_computation/rf/1rfx/1rfx.fit
pddf	/app/data/pr_computation/rf/1rfx/1rfx.pr.out
profile	/app/data/saxs_computation/rf/1rfx/1rfx.dat

Crystal Structure of resisitin

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) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)