2jkv

Structure of human Phosphogluconate Dehydrogenase in complex with NADPH at 2.53A

Method: X-RAY DIFFRACTION D_max: 204.5 Å Quality: REASONABLE

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	2jkv
沉积日期 deposition_date	2008-09-01
结构标题 title	Structure of human Phosphogluconate Dehydrogenase in complex with NADPH at 2.53A
关键词 keywords	OXIDOREDUCTASE, PHOSPHOGLUCONATE, NADP, NADPH, PENTOSE SHUNT, DEHYDROGENASE; 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	63.39 Å
回转半径 Rg (电子) rg_electron	64.83 Å
零角强度 I(0) i0	1477340000.00
分子量 molecular_weight	319390.0 kDa
排除体积 excluded_volume	398620 Å³
包络体积 envelope_volume	554980 Å³
水化壳体积 shell_volume	80409 Å³
包络直径 envelope_diameter	229.1 Å
壳层 Rg shell_rg	53.03 Å
包络 Rg envelope_rg	63.76 Å
形状 Rg shape_rg	64.83 Å
总 Rg total_rg	64.53 Å
总原子数 total_atoms	22414
残基数 n_residues	2881
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	204.5 Å
Rg (实空间) rg_real	64.54 Å
Rg 误差 (实空间) rg_real_error	1.94 Å
I(0) (实空间) i0_real	1.4770e+09
I(0) 误差 (实空间) i0_real_error	3.1290e+07
Rg (倒空间) rg_reciprocal	62.28 Å
I(0) (倒空间) i0_reciprocal	1471000000.0000
解质量估计 total_estimate	0.5378
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	40.9 Å
偏度 Skewness skewness	0.602
峰度 Kurtosis kurtosis	-0.410
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0007
最高正则化参数 α highest_alpha	53320000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.725; Stabil: 0.998; Sysdev: 0.004; Positv: 1.000; Valcen: 0.773; Smooth: 0.030

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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	6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
分子量 formula_weight	55763.6 kDa
EC 编号 ec_number	1.1.1.44
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	23837

MHHHHHHSSGVDLGTENLYFQSMAQADIALIGLAVMGQNLILNMNDHGFVVCAFNRTVSKVDDFLANEAKGTKVVGAQSLKEMVSKLKKPRRIILLVKAGQAVDDFIEKLVPLLDTGDIIIDGGNSEYRDTTRRCRDLKAKGILFVGSGVSGGEEGARYGPSLMPGGNKEAWPHIKTIFQGIAAKVGTGEPCCDWVGDEGAGHFVKMVHNGIEYGDMQLICEAYHLMKDVLGMAQDEMAQAFEDWNKTELDSFLIEITANILKFQDTDGKHLLPKIRDSAGQKGTGKWTAISALEYGVPVTLIGEAVFARCLSSLKDERIQASKKLKGPQKFQFDGDKKSFLEDIRKALYASKIISYAQGFMLLRQAATEFGWTLNYGGIALMWRGGCIIRSVFLGKIKDAFDRNPELQNLLLDDFFKSAVENCQDSWRRAVSTGVQAGIPMPCFTTALSFYDGYRHEMLPASLIQAQRDYFGAHTYELLAKPGQFIHTNWTGHGGTVSSSSYNA

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

Entity 4 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	12

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	1405

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6. 折叠分类 (SCOP + CATH) 29 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d2jkva1
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	d2jkva2
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	d2jkvb1
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	d2jkvb2
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	d2jkvc1
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	d2jkvc2
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	d2jkvd1
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	d2jkvd2
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	d2jkve1
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	d2jkve2
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	d2jkvf1
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	d2jkvf2
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

CATH v4.4 (17 domains)

结构域编号 domain_id	2jkvA01
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	2jkvA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1040 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2

结构域编号 domain_id	2jkvA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	320 — 6-Phosphogluconate Dehydrogenase, domain 3

结构域编号 domain_id	2jkvB01
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	2jkvB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1040 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2

结构域编号 domain_id	2jkvB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	320 — 6-Phosphogluconate Dehydrogenase, domain 3

结构域编号 domain_id	2jkvC01
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	2jkvC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1040 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2

结构域编号 domain_id	2jkvC03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	320 — 6-Phosphogluconate Dehydrogenase, domain 3

结构域编号 domain_id	2jkvD01
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	2jkvD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1040 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2

结构域编号 domain_id	2jkvD03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	320 — 6-Phosphogluconate Dehydrogenase, domain 3

结构域编号 domain_id	2jkvE01
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	2jkvE02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1040 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2

结构域编号 domain_id	2jkvE03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	320 — 6-Phosphogluconate Dehydrogenase, domain 3

结构域编号 domain_id	2jkvF01
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	2jkvF02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1040 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	56.643 Å
晶胞边长 b length_b	204.714 Å
晶胞边长 c length_c	170.319 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.65 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

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	2.532 Å
最低分辨率 resolution_low	36.899 Å
R 因子 r_factor	0.1566
R_work r_work	0.1558
R_free r_free	0.2069

fit	/app/data/saxs_computation/jk/2jkv/2jkv.fit
pddf	/app/data/pr_computation/jk/2jkv/2jkv.pr.out
profile	/app/data/saxs_computation/jk/2jkv/2jkv.dat