SAXSdb — 2h63

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2h63
沉积日期 deposition_date	2006-05-30
结构标题 title	Crystal Structure of Human Biliverdin Reductase A
关键词 keywords	Oxidoreductase, Biliverdin reductase, BLVRA, Structural Genomics, Structural Genomics Consortium, SGC; OXIDOREDUCTASE
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	38.13 Å
回转半径 Rg (电子) rg_electron	37.99 Å
零角强度 I(0) i0	222928000.00
分子量 molecular_weight	122710.0 kDa
排除体积 excluded_volume	154310 Å³
包络体积 envelope_volume	203940 Å³
水化壳体积 shell_volume	46462 Å³
包络直径 envelope_diameter	132.2 Å
壳层 Rg shell_rg	42.27 Å
包络 Rg envelope_rg	37.31 Å
形状 Rg shape_rg	37.99 Å
总 Rg total_rg	38.26 Å
总原子数 total_atoms	8645
残基数 n_residues	1131
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	130.7 Å
Rg (实空间) rg_real	38.30 Å
Rg 误差 (实空间) rg_real_error	1.28 Å
I(0) (实空间) i0_real	2.2290e+08
I(0) 误差 (实空间) i0_real_error	3.7470e+06
Rg (倒空间) rg_reciprocal	38.20 Å
I(0) (倒空间) i0_reciprocal	222900000.0000
解质量估计 total_estimate	0.8715
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	44.6 Å
偏度 Skewness skewness	0.419
峰度 Kurtosis kurtosis	-0.359
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	37450000.0000
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: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.882

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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	Biliverdin reductase A
分子量 formula_weight	33020.0 kDa
EC 编号 ec_number	1.3.1.24
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	8668

SMRKFGVVVVGVGRAGSVRMRDLRNPHPSSAFLNLIGFVSRRELGSIDGVQQISLEDALSSQEVEVAYICSESSSHEDYIRQFLNAGKHVLVEYPMTLSLAAAQELWELAEQKGKVLHEEHVELLMEEFAFLKKEVVGKDLLKGSLLFTAGPLEEERFGFPAFSGISRLTWLVSLFGELSLVSATLEERKEDQYMKMTVCLETEKKSPLSWIEEKGPGLKRNRYLSFHFKSGSLENVPNVGVNKNIFLKDQNIFVQKLLGQFSEKELAAEKKRILHCLGLAEEIQKYCCSRK

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	Escherichia coli

Entity 2 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 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	23

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6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

结构域编号 domain_id	2h63A01
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	2h63A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	2h63B01
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	2h63B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	2h63C01
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	2h63C02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	2h63D01
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	2h63D02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	90.787 Å
晶胞边长 b length_b	92.747 Å
晶胞边长 c length_c	147.755 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	16

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2394
R_work r_work	0.2374
R_free r_free	0.2869

fit	/app/data/saxs_computation/h6/2h63/2h63.fit
pddf	/app/data/pr_computation/h6/2h63/2h63.pr.out
profile	/app/data/saxs_computation/h6/2h63/2h63.dat

Crystal Structure of Human Biliverdin Reductase A

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