SAXSdb — 1fur

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1fur
沉积日期 deposition_date	1997-01-09
结构标题 title	FUMARASE MUTANT H188N WITH BOUND SUBSTRATE L-MALATE AT PUTATIVE ACTIVATOR SITE
关键词 keywords	;HYDROLYASE, CARBON OXYGEN LYASE, KREB'S CYCLE ENZYME, FUMARATE HYDRATASE ;; HYDROLYASE
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	36.00 Å
回转半径 Rg (电子) rg_electron	35.34 Å
零角强度 I(0) i0	157027000.00
分子量 molecular_weight	98883.0 kDa
排除体积 excluded_volume	123050 Å³
包络体积 envelope_volume	158210 Å³
水化壳体积 shell_volume	37658 Å³
包络直径 envelope_diameter	109.8 Å
壳层 Rg shell_rg	41.24 Å
包络 Rg envelope_rg	34.78 Å
形状 Rg shape_rg	35.38 Å
总 Rg total_rg	35.61 Å
总原子数 total_atoms	8489
残基数 n_residues	911
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	108.9 Å
Rg (实空间) rg_real	35.90 Å
Rg 误差 (实空间) rg_real_error	0.71 Å
I(0) (实空间) i0_real	1.5700e+08
I(0) 误差 (实空间) i0_real_error	2.3480e+06
Rg (倒空间) rg_reciprocal	35.97 Å
I(0) (倒空间) i0_reciprocal	157000000.0000
解质量估计 total_estimate	0.8975
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	47.0 Å
偏度 Skewness skewness	0.070
峰度 Kurtosis kurtosis	-0.844
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	13100000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.768

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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	FUMARASE C
分子量 formula_weight	50524.7 kDa
EC 编号 ec_number	4.2.1.2
突变 mutation	H188N
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	9695

MNTVRSEKDSMGAIDVPADKLWGAQTQRSLEHFRISTEKMPTSLIHALALTKRAAAKVNEDLGLLSEEKASAIRQAADEVLAGQHDDEFPLAIWQTGSGTQSNMNMNEVLANRASELLGGVRGMERKVHPNDDVNKSQSSNDVFPTAMHVAALLALRKQLIPQLKTLTQTLNEKSRAFADIVKIGRTNLQDATPLTLGQEISGWVAMLEHNLKHIEYSLPHVAELALGGTAVGTGLNTHPEYARRVADELAVITCAPFVTAPNKFEALATCDALVQAHGALKGLAASLMKIANDVRWLASGPRCGIGEISIPENEPGSSIMPGKVNPTQCEALTMLCCQVMGNDVAINMGGASGNFELNVFRPMVIHNFLQSVRLLADGMESFNKHCAVGIEPNRERINQLLNESLMLVTALNTHIGYDKAAEIAKKAHKEGLTLKAAALALGYLSEAEFDSWVRPEQMVGSMKAGR

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	D-MALATE
分子量 formula_weight	134.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	402

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1fura_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.127 — L-aspartase-like
超家族 Superfamily superfamily	a.127.1 — L-aspartase-like
家族 Family family	a.127.1.1 — L-aspartase/fumarase

结构域编号 domain_id	d1furb_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.127 — L-aspartase-like
超家族 Superfamily superfamily	a.127.1 — L-aspartase-like
家族 Family family	a.127.1.1 — L-aspartase/fumarase

CATH v4.4 (6 domains)

结构域编号 domain_id	1furA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	275 — Fumarase C; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

结构域编号 domain_id	1furA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	200 — Fumarase C; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

结构域编号 domain_id	1furA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	40 — Ribonucleotide Reductase Protein R1; domain 1
同源超家族 H-superfamily homologous superfamily	30 — Fumarase/aspartase (C-terminal domain)

结构域编号 domain_id	1furB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	275 — Fumarase C; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

结构域编号 domain_id	1furB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	200 — Fumarase C; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

结构域编号 domain_id	1furB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	40 — Ribonucleotide Reductase Protein R1; domain 1
同源超家族 H-superfamily homologous superfamily	30 — Fumarase/aspartase (C-terminal domain)

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7. 引用文献 (1)

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晶胞边长 a length_a	104.030 Å
晶胞边长 b length_b	219.320 Å
晶胞边长 c length_c	86.540 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	1.950 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.1700
R_work r_work	0.1700
R_free r_free	0.2090

fit	/app/data/saxs_computation/fu/1fur/1fur.fit
pddf	/app/data/pr_computation/fu/1fur/1fur.pr.out
profile	/app/data/saxs_computation/fu/1fur/1fur.dat

FUMARASE MUTANT H188N WITH BOUND SUBSTRATE L-MALATE AT PUTATIVE ACTIVATOR SITE

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