SAXSdb — 1k8c

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1k8c
沉积日期 deposition_date	2001-10-23
结构标题 title	Crystal structure of dimeric xylose reductase in complex with NADP(H)
关键词 keywords	beta-alpha barrel, aldo-keto reductase, NADP(H), 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	41.68 Å
回转半径 Rg (电子) rg_electron	41.38 Å
零角强度 I(0) i0	294282000.00
分子量 molecular_weight	145620.0 kDa
排除体积 excluded_volume	184260 Å³
包络体积 envelope_volume	229740 Å³
水化壳体积 shell_volume	48171 Å³
包络直径 envelope_diameter	141.5 Å
壳层 Rg shell_rg	44.10 Å
包络 Rg envelope_rg	41.15 Å
形状 Rg shape_rg	41.36 Å
总 Rg total_rg	41.61 Å
总原子数 total_atoms	10303
残基数 n_residues	1274
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	139.2 Å
Rg (实空间) rg_real	41.92 Å
Rg 误差 (实空间) rg_real_error	1.19 Å
I(0) (实空间) i0_real	2.9430e+08
I(0) 误差 (实空间) i0_real_error	5.3110e+06
Rg (倒空间) rg_reciprocal	41.68 Å
I(0) (倒空间) i0_reciprocal	294200000.0000
解质量估计 total_estimate	0.8337
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	40.3 Å
偏度 Skewness skewness	0.451
峰度 Kurtosis kurtosis	-0.441
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	42130000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.913; Smooth: 0.333

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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	xylose reductase
分子量 formula_weight	36062.2 kDa
EC 编号 ec_number	1.1.1.21
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	11037

MSASIPDIKLSSGHLMPSIGFGCWKLANATAGEQVYQAIKAGYRLFDGAEDYGNEKEVGDGVKRAIDEGLVKREEIFLTSKLWNNYHDPKNVETALNKTLADLKVDYVDLFLIHFPIAFKFVPIEEKYPPGFYCGDGNNFVYEDVPILETWKALEKLVAAGKIKSIGVSNFPGALLLDLLRGATIKPAVLQVEHHPYLQQPKLIEFAQKAGVTITAYSSFGPQSFVEMNQGRALNTPTLFAHDTIKAIAAKYNKTPAEVLLRWAAQRGIAVIPKSNLPERLVQNRSFNTFDLTKEDFEEIAKLDIGLRFNDPWDWDNIPIFV

来源 Source

来源生物 organism	Candida tenuis
NCBI 分类编号 ncbi_taxonomy_id	45596
宿主生物 host_organism	Escherichia coli BL21(DE3)

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	734

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1k8ca_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.7 — NAD(P)-linked oxidoreductase
家族 Family family	c.1.7.1 — Aldo-keto reductases (NADP)

结构域编号 domain_id	d1k8cb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.7 — NAD(P)-linked oxidoreductase
家族 Family family	c.1.7.1 — Aldo-keto reductases (NADP)

结构域编号 domain_id	d1k8cc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.7 — NAD(P)-linked oxidoreductase
家族 Family family	c.1.7.1 — Aldo-keto reductases (NADP)

结构域编号 domain_id	d1k8cd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.7 — NAD(P)-linked oxidoreductase
家族 Family family	c.1.7.1 — Aldo-keto reductases (NADP)

CATH v4.4 (4 domains)

结构域编号 domain_id	1k8cA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	100 — NADP-dependent oxidoreductase domain

结构域编号 domain_id	1k8cB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	100 — NADP-dependent oxidoreductase domain

结构域编号 domain_id	1k8cC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	100 — NADP-dependent oxidoreductase domain

结构域编号 domain_id	1k8cD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	100 — NADP-dependent oxidoreductase domain

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7. 引用文献 (1)

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晶胞边长 a length_a	182.202 Å
晶胞边长 b length_b	127.809 Å
晶胞边长 c length_c	80.251 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.37 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

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	2.100 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.2130
R_free r_free	0.2430

fit	/app/data/saxs_computation/k8/1k8c/1k8c.fit
pddf	/app/data/pr_computation/k8/1k8c/1k8c.pr.out
profile	/app/data/saxs_computation/k8/1k8c/1k8c.dat

Crystal structure of dimeric xylose reductase in complex with NADP(H)

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