SAXSdb — 1gnj

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1gnj
沉积日期 deposition_date	2001-10-05
结构标题 title	HUMAN SERUM ALBUMIN COMPLEXED WITH cis-5,8,11,14-EICOSATETRAENOIC ACID (ARACHIDONIC ACID)
关键词 keywords	PLASMA PROTEIN, METAL-BINDING, LIPID-BINDING, GLYCOPROTEIN; PLASMA PROTEIN
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	28.99 Å
回转半径 Rg (电子) rg_electron	27.89 Å
零角强度 I(0) i0	69671100.00
分子量 molecular_weight	66594.0 kDa
排除体积 excluded_volume	83847 Å³
包络体积 envelope_volume	105870 Å³
水化壳体积 shell_volume	32293 Å³
包络直径 envelope_diameter	95.3 Å
壳层 Rg shell_rg	34.63 Å
包络 Rg envelope_rg	27.74 Å
形状 Rg shape_rg	27.89 Å
总 Rg total_rg	28.59 Å
总原子数 total_atoms	4670
残基数 n_residues	582
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	89.9 Å
Rg (实空间) rg_real	28.92 Å
Rg 误差 (实空间) rg_real_error	0.60 Å
I(0) (实空间) i0_real	6.9670e+07
I(0) 误差 (实空间) i0_real_error	1.0810e+06
Rg (倒空间) rg_reciprocal	28.95 Å
I(0) (倒空间) i0_reciprocal	69670000.0000
解质量估计 total_estimate	0.9072
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	34.3 Å
偏度 Skewness skewness	0.221
峰度 Kurtosis kurtosis	-0.526
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	9459000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.903

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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	SERUM ALBUMIN
分子量 formula_weight	66571.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	4679

DAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEPERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTLSEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLVAASQAALGL

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	SACCHAROMYCES CEREVISIAE

Entity 2 non-polymer

描述 description	ARACHIDONIC ACID
分子量 formula_weight	304.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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	9

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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	d1gnja1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.126 — Serum albumin-like
超家族 Superfamily superfamily	a.126.1 — Serum albumin-like
家族 Family family	a.126.1.1 — Serum albumin-like

结构域编号 domain_id	d1gnja2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.126 — Serum albumin-like
超家族 Superfamily superfamily	a.126.1 — Serum albumin-like
家族 Family family	a.126.1.1 — Serum albumin-like

结构域编号 domain_id	d1gnja3
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.126 — Serum albumin-like
超家族 Superfamily superfamily	a.126.1 — Serum albumin-like
家族 Family family	a.126.1.1 — Serum albumin-like

CATH v4.4 (6 domains)

结构域编号 domain_id	1gnjA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	246 — Serum Albumin; Chain A, Domain 1
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1gnjA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	246 — Serum Albumin; Chain A, Domain 1
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1gnjA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	246 — Serum Albumin; Chain A, Domain 1
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1gnjA04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	246 — Serum Albumin; Chain A, Domain 1
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1gnjA05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	246 — Serum Albumin; Chain A, Domain 1
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1gnjA06
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	246 — Serum Albumin; Chain A, Domain 1
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	190.219 Å
晶胞边长 b length_b	38.972 Å
晶胞边长 c length_c	96.236 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	105.75 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	29.620 Å
R 因子 r_factor	0.1940
R_work r_work	0.1940
R_free r_free	0.2450

fit	/app/data/saxs_computation/gn/1gnj/1gnj.fit
pddf	/app/data/pr_computation/gn/1gnj/1gnj.pr.out
profile	/app/data/saxs_computation/gn/1gnj/1gnj.dat

HUMAN SERUM ALBUMIN COMPLEXED WITH cis-5,8,11,14-EICOSATETRAENOIC ACID (ARACHIDONIC ACID)

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