SAXSdb — 1vme

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1vme
沉积日期 deposition_date	2004-09-21
结构标题 title	Crystal structure of Flavoprotein (TM0755) from Thermotoga maritima at 1.80 A resolution
关键词 keywords	;TM0755, FLAVOPROTEIN, STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, Joint Center for Structural Genomics, ELECTRON TRANSPORT ;; ELECTRON TRANSPORT
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	31.03 Å
回转半径 Rg (电子) rg_electron	30.46 Å
零角强度 I(0) i0	117905000.00
分子量 molecular_weight	90239.0 kDa
排除体积 excluded_volume	114250 Å³
包络体积 envelope_volume	134140 Å³
水化壳体积 shell_volume	36886 Å³
包络直径 envelope_diameter	111.9 Å
壳层 Rg shell_rg	37.08 Å
包络 Rg envelope_rg	30.51 Å
形状 Rg shape_rg	30.46 Å
总 Rg total_rg	31.03 Å
总原子数 total_atoms	6322
残基数 n_residues	782
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	103.8 Å
Rg (实空间) rg_real	31.11 Å
Rg 误差 (实空间) rg_real_error	0.93 Å
I(0) (实空间) i0_real	1.1790e+08
I(0) 误差 (实空间) i0_real_error	2.0190e+06
Rg (倒空间) rg_reciprocal	31.08 Å
I(0) (倒空间) i0_reciprocal	117900000.0000
解质量估计 total_estimate	0.8689
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	32.6 Å
偏度 Skewness skewness	0.428
峰度 Kurtosis kurtosis	-0.291
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	70000000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.921; Smooth: 0.822

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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	Flavoprotein
分子量 formula_weight	47123.0 kDa
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	7037

MGSDKIHHHHHHMPKIWTERIFDDPEIYVLRIDDDRIRYFEAVWEIPEGISYNAYLVKLNGANVLIDGWKGNYAKEFIDALSKIVDPKEITHIIVNHTEPDHSGSLPATLKTIGHDVEIIASNFGKRLLEGFYGIKDVTVVKDGEEREIGGKKFKFVMTPWLHWPDTMVTYLDGILFSCDVGGGYLLPEILDDSNESVVERYLPHVTKYIVTVIGHYKNYILEGAEKLSSLKIKALLPGHGLIWKKDPQRLLNHYVSVAKGDPKKGKVTVIYDSMYGFVENVMKKAIDSLKEKGFTPVVYKFSDEERPAISEILKDIPDSEALIFGVSTYEAEIHPLMRFTLLEIIDKANYEKPVLVFGVHGWAPSAERTAGELLKETKFRILSFTEIKGSNMDERKIEEAISLLKKELE

来源 Source

来源生物 organism	Thermotoga maritima
NCBI 分类编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli

Entity 2 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	3

Entity 3 non-polymer

描述 description	MU-OXO-DIIRON
分子量 formula_weight	127.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	442

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1vmea1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.5 — Flavoproteins
家族 Family family	c.23.5.1 — Flavodoxin-related

结构域编号 domain_id	d1vmea2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
超家族 Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
家族 Family family	d.157.1.3 — ROO N-terminal domain-like

结构域编号 domain_id	d1vmea3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1vmeb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.5 — Flavoproteins
家族 Family family	c.23.5.1 — Flavodoxin-related

结构域编号 domain_id	d1vmeb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
超家族 Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
家族 Family family	d.157.1.3 — ROO N-terminal domain-like

结构域编号 domain_id	d1vmeb3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

结构域编号 domain_id	1vmeA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	15 — Metallo-beta-lactamase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

结构域编号 domain_id	1vmeA02
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	360 — Flavodoxin domain

结构域编号 domain_id	1vmeB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	15 — Metallo-beta-lactamase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

结构域编号 domain_id	1vmeB02
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	360 — Flavodoxin domain

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7. 引用文献 (1)

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晶胞边长 a length_a	55.242 Å
晶胞边长 b length_b	95.831 Å
晶胞边长 c length_c	90.130 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	95.43 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	1.800 Å
最低分辨率 resolution_low	48.920 Å
R 因子 r_factor	0.1486
R_work r_work	0.1469
R_free r_free	0.1810

fit	/app/data/saxs_computation/vm/1vme/1vme.fit
pddf	/app/data/pr_computation/vm/1vme/1vme.pr.out
profile	/app/data/saxs_computation/vm/1vme/1vme.dat

Crystal structure of Flavoprotein (TM0755) from Thermotoga maritima at 1.80 A resolution

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution