2gra

crystal structure of Human Pyrroline-5-carboxylate Reductase complexed with nadp

Method: X-RAY DIFFRACTION D_max: 119.3 Å Quality: EXCELLENT

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2gra
沉积日期 deposition_date	2006-04-23
结构标题 title	crystal structure of Human Pyrroline-5-carboxylate Reductase complexed with nadp
关键词 keywords	Human Pyrroline-5-carboxylate Reductase, NADPH, OXIDOREDUCTASE; 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	40.10 Å
回转半径 Rg (电子) rg_electron	39.36 Å
零角强度 I(0) i0	358203000.00
分子量 molecular_weight	149610.0 kDa
排除体积 excluded_volume	186110 Å³
包络体积 envelope_volume	288460 Å³
水化壳体积 shell_volume	60569 Å³
包络直径 envelope_diameter	117.7 Å
壳层 Rg shell_rg	46.66 Å
包络 Rg envelope_rg	36.89 Å
形状 Rg shape_rg	39.35 Å
总 Rg total_rg	39.84 Å
总原子数 total_atoms	10459
残基数 n_residues	1383
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	119.3 Å
Rg (实空间) rg_real	39.86 Å
Rg 误差 (实空间) rg_real_error	0.65 Å
I(0) (实空间) i0_real	3.5820e+08
I(0) 误差 (实空间) i0_real_error	6.1340e+06
Rg (倒空间) rg_reciprocal	40.09 Å
I(0) (倒空间) i0_reciprocal	358300000.0000
解质量估计 total_estimate	0.9109
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	52.0 Å
偏度 Skewness skewness	-0.026
峰度 Kurtosis kurtosis	-0.666
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	27290000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.966; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.965

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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 (4)

Entity 1 polymer

描述 description	Pyrroline-5-carboxylate reductase 1
分子量 formula_weight	29147.6 kDa
EC 编号 ec_number	1.5.1.2
来源方法 src_method	man
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E
原子数 atom_count	11079

RGMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMADQE

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	5

Entity 3 non-polymer

描述 description	GLUTAMIC ACID
分子量 formula_weight	147.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 4 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	620

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6. 折叠分类 (SCOP + CATH) 25 domains

SCOP 2.08 (15 domains)

结构域编号 domain_id	d2graa1
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.2.1.0 — automated matches

结构域编号 domain_id	d2graa2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
超家族 Superfamily superfamily	a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
家族 Family family	a.100.1.0 — automated matches

结构域编号 domain_id	d2graa3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2grab1
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.2.1.0 — automated matches

结构域编号 domain_id	d2grab2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
超家族 Superfamily superfamily	a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
家族 Family family	a.100.1.0 — automated matches

结构域编号 domain_id	d2grab3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2grac1
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.2.1.0 — automated matches

结构域编号 domain_id	d2grac2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
超家族 Superfamily superfamily	a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
家族 Family family	a.100.1.0 — automated matches

结构域编号 domain_id	d2grac3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2grad1
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.2.1.0 — automated matches

结构域编号 domain_id	d2grad2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
超家族 Superfamily superfamily	a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
家族 Family family	a.100.1.0 — automated matches

结构域编号 domain_id	d2grad3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2grae1
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.2.1.0 — automated matches

结构域编号 domain_id	d2grae2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
超家族 Superfamily superfamily	a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
家族 Family family	a.100.1.0 — automated matches

结构域编号 domain_id	d2grae3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (10 domains)

结构域编号 domain_id	2graA01
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	2graA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3730 — ProC C-terminal domain-like fold
同源超家族 H-superfamily homologous superfamily	10 — ProC C-terminal domain-like

结构域编号 domain_id	2graB01
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	2graB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3730 — ProC C-terminal domain-like fold
同源超家族 H-superfamily homologous superfamily	10 — ProC C-terminal domain-like

结构域编号 domain_id	2graC01
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	2graC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3730 — ProC C-terminal domain-like fold
同源超家族 H-superfamily homologous superfamily	10 — ProC C-terminal domain-like

结构域编号 domain_id	2graD01
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	2graD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3730 — ProC C-terminal domain-like fold
同源超家族 H-superfamily homologous superfamily	10 — ProC C-terminal domain-like

结构域编号 domain_id	2graE01
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	2graE02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3730 — ProC C-terminal domain-like fold
同源超家族 H-superfamily homologous superfamily	10 — ProC C-terminal domain-like

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7. 引用文献 (1)

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晶胞边长 a length_a	207.868 Å
晶胞边长 b length_b	123.502 Å
晶胞边长 c length_c	120.826 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	121.97 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	20

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	3.100 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2300
R_work r_work	0.2280
R_free r_free	0.2490

fit	/app/data/saxs_computation/gr/2gra/2gra.fit
pddf	/app/data/pr_computation/gr/2gra/2gra.pr.out
profile	/app/data/saxs_computation/gr/2gra/2gra.dat