SAXSdb — 1ik3

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ik3
沉积日期 deposition_date	2001-05-01
结构标题 title	LIPOXYGENASE-3 (SOYBEAN) COMPLEX WITH 13(S)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID
关键词 keywords	OXIDOREDUCTASE, PURPLE LIPOXYGENASE, FE(III) COMPLEX, INTERM; 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	29.34 Å
回转半径 Rg (电子) rg_electron	28.45 Å
零角强度 I(0) i0	138649000.00
分子量 molecular_weight	95109.0 kDa
排除体积 excluded_volume	119670 Å³
包络体积 envelope_volume	143260 Å³
水化壳体积 shell_volume	41052 Å³
包络直径 envelope_diameter	103.4 Å
壳层 Rg shell_rg	36.69 Å
包络 Rg envelope_rg	28.73 Å
形状 Rg shape_rg	28.43 Å
总 Rg total_rg	29.25 Å
总原子数 total_atoms	6719
残基数 n_residues	836
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	98.3 Å
Rg (实空间) rg_real	29.30 Å
Rg 误差 (实空间) rg_real_error	0.85 Å
I(0) (实空间) i0_real	1.3860e+08
I(0) 误差 (实空间) i0_real_error	1.9840e+06
Rg (倒空间) rg_reciprocal	29.32 Å
I(0) (倒空间) i0_reciprocal	138700000.0000
解质量估计 total_estimate	0.7978
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	34.6 Å
偏度 Skewness skewness	0.390
峰度 Kurtosis kurtosis	-0.140
角度范围 angular_range	— – 0.2700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	39950000.0000
实空间数据点数 n_real_points	55
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.789; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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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 (7)

Entity 1 polymer

描述 description	LIPOXYGENASE-3
分子量 formula_weight	96919.0 kDa
EC 编号 ec_number	1.13.11.12
来源方法 src_method	nat
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	7314

MLGGLLHRGHKIKGTVVLMRKNVLDVNSVTSVGGIIGQGLDLVGSTLDTLTAFLGRSVSLQLISATKADANGKGKLGKATFLEGIITSLPTLGAGQSAFKINFEWDDGSGIPGAFYIKNFMQTEFFLVSLTLEDIPNHGSIHFVCNSWIYNAKLFKSDRIFFANQTYLPSETPAPLVKYREEELHNLRGDGTGERKEWERIYDYDVYNDLGDPDKGENHARPVLGGNDTFPYPRRGRTGRKPTRKDPNSESRSNDVYLPRDEAFGHLKSSDFLTYGLKSVSQNVLPLLQSAFDLNFTPREFDSFDEVHGLYSGGIKLPTDIISKISPLPVLKEIFRTDGEQALKFPPPKVIQVSKSAWMTDEEFAREMLAGVNPNLIRCLKDFPPRSKLDSQVYGDHTSQITKEHLEPNLEGLTVDEAIQNKRLFLLDHHDPIMPYLRRINATSTKAYATRTILFLKNDGTLRPLAIELSLPHPQGDQSGAFSQVFLPADEGVESSIWLLAKAYVVVNDSCYHQLVSHWLNTHAVVEPFIIATNRHLSVVHPIYKLLHPHYRDTMNINGLARLSLVNDGGVIEQTFLWGRYSVEMSAVVYKDWVFTDQALPADLIKRGMAIEDPSCPHGIRLVIEDYPYTVDGLEIWDAIKTWVHEYVFLYYKSDDTLREDPELQACWKELVEVGHGDKKNEPWWPKMQTREELVEACAIIIWTASALHAAVNFGQYPYGGLILNRPTLSRRFMPEKGSAEYEELRKNPQKAYLKTITPKFQTLIDLSVIEILSRHASDEVYLGERDNPNWTSDTRALEAFKRFGNKLAQIENKLSERNNDEKLRNRCGPVQMPYTLLLPSSKEGLTFRGIPNSISI

Entity 2 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	13(S)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID
分子量 formula_weight	312.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	13(R)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID
分子量 formula_weight	312.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	(TRANS-12,13-EPOXY)-9-HYDROXY-10(E)-OCTADECENOIC ACID
分子量 formula_weight	312.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	(TRANS-12,13-EPOXY)-11-HYDROXY-9(Z)-OCTADECENOIC ACID
分子量 formula_weight	312.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 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	529

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6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1ik3a1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.119 — Lipoxigenase
超家族 Superfamily superfamily	a.119.1 — Lipoxigenase
家族 Family family	a.119.1.1 — Plant lipoxigenases

结构域编号 domain_id	d1ik3a2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.12 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
超家族 Superfamily superfamily	b.12.1 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
家族 Family family	b.12.1.1 — Lipoxigenase N-terminal domain

CATH v4.4 (5 domains)

结构域编号 domain_id	1ik3A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	60 — Lipoxygenase-1
同源超家族 H-superfamily homologous superfamily	20 — PLAT/LH2 domain

结构域编号 domain_id	1ik3A02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	375 — Lipoxygenase-1; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lipoxygenase-1; Domain 2

结构域编号 domain_id	1ik3A03
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	372 — Lipoxygenase-1; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Lipoxygenase-1; Domain 3

结构域编号 domain_id	1ik3A04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	60 —

结构域编号 domain_id	1ik3A05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	245 — Lipoxygenase-1; domain 5
同源超家族 H-superfamily homologous superfamily	10 — Lipoxygenase-1; Domain 5

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7. 引用文献 (4)

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晶胞边长 a length_a	112.650 Å
晶胞边长 b length_b	137.280 Å
晶胞边长 c length_c	61.890 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	95.56 °
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	2.000 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.1960
R_work r_work	0.1960
R_free r_free	0.2960

fit	/app/data/saxs_computation/ik/1ik3/1ik3.fit
pddf	/app/data/pr_computation/ik/1ik3/1ik3.pr.out
profile	/app/data/saxs_computation/ik/1ik3/1ik3.dat

LIPOXYGENASE-3 (SOYBEAN) COMPLEX WITH 13(S)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution