SAXSdb — 1fgm

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1fgm
沉积日期 deposition_date	2000-07-28
结构标题 title	LIPOXYGENASE-1 (SOYBEAN) AT 100K, N694H MUTANT
关键词 keywords	DIOXYGENASE, LIPOXYGENASE, METALLOPROTEIN, FATTY ACIDS, 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	28.88 Å
回转半径 Rg (电子) rg_electron	28.00 Å
零角强度 I(0) i0	129807000.00
分子量 molecular_weight	92307.0 kDa
排除体积 excluded_volume	116330 Å³
包络体积 envelope_volume	137560 Å³
水化壳体积 shell_volume	40011 Å³
包络直径 envelope_diameter	100.6 Å
壳层 Rg shell_rg	36.25 Å
包络 Rg envelope_rg	28.31 Å
形状 Rg shape_rg	27.97 Å
总 Rg total_rg	28.85 Å
总原子数 total_atoms	6520
残基数 n_residues	818
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	95.9 Å
Rg (实空间) rg_real	28.85 Å
Rg 误差 (实空间) rg_real_error	0.56 Å
I(0) (实空间) i0_real	1.2980e+08
I(0) 误差 (实空间) i0_real_error	1.8700e+06
Rg (倒空间) rg_reciprocal	28.87 Å
I(0) (倒空间) i0_reciprocal	129800000.0000
解质量估计 total_estimate	0.8776
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	33.1 Å
偏度 Skewness skewness	0.389
峰度 Kurtosis kurtosis	-0.164
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	38950000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.973

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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	SEED LIPOXYGENASE-1
分子量 formula_weight	94504.2 kDa
EC 编号 ec_number	1.13.11.12
突变 mutation	N694H
来源方法 src_method	man
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	7248

MFSAGHKIKGTVVLMPKNELEVNPDGSAVDNLNAFLGRSVSLQLISATKADAHGKGKVGKDTFLEGINTSLPTLGAGESAFNIHFEWDGSMGIPGAFYIKNYMQVEFFLKSLTLEAISNQGTIRFVCNSWVYNTKLYKSVRIFFANHTYVPSETPAPLVSYREEELKSLRGNGTGERKEYDRIYDYDVYNDLGNPDKSEKLARPVLGGSSTFPYPRRGRTGRGPTVTDPNTEKQGEVFYVPRDENLGHLKSKDALEIGTKSLSQIVQPAFESAFDLKSTPIEFHSFQDVHDLYEGGIKLPRDVISTIIPLPVIKELYRTDGQHILKFPQPHVVQVSQSAWMTDEEFAREMIAGVNPCVIRGLEEFPPKSNLDPAIYGDQSSKITADSLDLDGYTMDEALGSRRLFMLDYHDIFMPYVRQINQLNSAKTYATRTILFLREDGTLKPVAIELSLPHSAGDLSAAVSQVVLPAKEGVESTIWLLAKAYVIVNDSCYHQLMSHWLNTHAAMEPFVIATHRHLSVLHPIYKLLTPHYRNNMNINALARQSLINANGIIETTFLPSKYSVEMSSAVYKNWVFTDQALPADLIKRGVAIKDPSTPHGVRLLIEDYPYAADGLEIWAAIKTWVQEYVPLYYARDDDVKNDSELQHWWKEAVEKGHGDLKDKPWWPKLQTLEDLVEVCLIIIWIASALHAAVHFGQYPYGGLIMNRPTASRRLLPEKGTPEYEEMINNHEKAYLRTITSKLPTLISLSVIEILSTHASDEVYLGQRDNPHWTSDSKALQAFQKFGNKLKEIEEKLVRRNNDPSLQGNRLGPVQLPYTLLYPSSEEGLTFRGIPNSISI

来源 Source

来源生物 organism	Glycine max
通用名 common_name	soybean
NCBI 分类编号 ncbi_taxonomy_id	3847
宿主生物 host_organism	Escherichia coli

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 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	681

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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	d1fgma1
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	d1fgma2
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	1fgmA01
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	1fgmA02
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	1fgmA03
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	1fgmA04
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	1fgmA05
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 (8)

Structural and functional characterization of second-coordination sphere mutants of soybean lipoxygenase-1.

Biochemistry (2001)

PMID: 11412104 · DOI: 10.1021/bi002893d PRIMARY

CRYSTAL STRUCTURE OF SOYBEAN LIPOXYGENASE L-1 AT 1.4 A RESOLUTION

Biochemistry (1996)

DOI: 10.1021/bi960576u

EXPERIMENTAL EVIDENCE FOR EXTENSIVE TUNNELING OF HYDROGEN IN THE LIPOXYGENASE REACTION: IMPLICATIONS FOR ENZYME CATALYSIS

J.Am.Chem.Soc. (1996)

DOI: 10.1021/ja961827p

NATURE OF THE RATE-LIMITING STEPS IN THE SOYBEAN LIPOXYGENASE-1 REACTION

Biochemistry (1995)

THE STRUCTURE AND FUNCTION OF LIPOXYGENASE

CURR.OPIN.STRUCT.BIOL. (1994)

THE THREE-DIMENSIONAL STRUCTURE OF AN ARACHIDONIC ACID 15-LIPOXYGENASE

Science (1993)

CRYSTALLOGRAPHIC DETERMINATION OF THE ACTIVE SITE IRON AND ITS LIGANDS IN SOYBEAN LIPOXYGENASE L-1

Biochemistry (1993)

CRYSTALLIZATION AND PRELIMINARY X-RAY INVESTIGATION OF LIPOXYGENASE 1 FROM SOYBEANS

J.Biol.Chem. (1990)

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晶胞边长 a length_a	94.260 Å
晶胞边长 b length_b	92.770 Å
晶胞边长 c length_c	49.230 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.22 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	2

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	1.900 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1890
R_work r_work	0.1783
R_free r_free	0.2124

fit	/app/data/saxs_computation/fg/1fgm/1fgm.fit
pddf	/app/data/pr_computation/fg/1fgm/1fgm.pr.out
profile	/app/data/saxs_computation/fg/1fgm/1fgm.dat

LIPOXYGENASE-1 (SOYBEAN) AT 100K, N694H MUTANT

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