SAXSdb — 1s4m

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1s4m
沉积日期 deposition_date	2004-01-16
结构标题 title	Crystal structure of flavin binding to FAD synthetase from Thermotoga maritina
关键词 keywords	;FAD, flavin, riboflavin kinase, Structural Genomics, BSGC structure funded by NIH, Protein Structure Initiative, PSI, Berkeley Structural Genomics Center, TRANSFERASE ;; TRANSFERASE
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	28.29 Å
回转半径 Rg (电子) rg_electron	27.35 Å
零角强度 I(0) i0	61347400.00
分子量 molecular_weight	63546.0 kDa
排除体积 excluded_volume	80654 Å³
包络体积 envelope_volume	101510 Å³
水化壳体积 shell_volume	30989 Å³
包络直径 envelope_diameter	97.5 Å
壳层 Rg shell_rg	34.73 Å
包络 Rg envelope_rg	27.20 Å
形状 Rg shape_rg	27.34 Å
总 Rg total_rg	28.16 Å
总原子数 total_atoms	4487
残基数 n_residues	549
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	91.3 Å
Rg (实空间) rg_real	28.21 Å
Rg 误差 (实空间) rg_real_error	0.59 Å
I(0) (实空间) i0_real	6.1350e+07
I(0) 误差 (实空间) i0_real_error	9.0280e+05
Rg (倒空间) rg_reciprocal	28.24 Å
I(0) (倒空间) i0_reciprocal	61350000.0000
解质量估计 total_estimate	0.9006
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	89.6 Å
偏度 Skewness skewness	0.220
峰度 Kurtosis kurtosis	-0.507
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	17890000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.953

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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 (4)

Entity 1 polymer

描述 description	riboflavin kinase/FMN adenylyltransferase
分子量 formula_weight	33665.8 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	4715

MVVSIGVFDGVHIGHQKVLRTMKEIAFFRKDDSLIYTISYPPEYFLPDFPGLLMTVESRVEMLSRYARTVVLDFFRIKDLTPEGFVERYLSGVSAVVVGRDFRFGKNASGNASFLRKKGVEVYEIEDVVVQGKRVSSSLIRNLVQEGRVEEIPAYLGRYFEIEGIVHKDREFGRKLGFPTANIDRGNEKLVDLKRGVYLVRVHLPDGKKKFGVMNVGFRPTVGDARNVKYEVYILDFEGDLYGQRLKLEVLKFMRDEKKFDSIEELKAAIDQDVKSARNMIDDIINSKFEKEG

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	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	LUMICHROME
分子量 formula_weight	242.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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	228

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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	d1s4ma1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamily	b.43.5 — Riboflavin kinase-like
家族 Family family	b.43.5.1 — ATP-dependent riboflavin kinase-like

结构域编号 domain_id	d1s4ma2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
家族 Family family	c.26.1.3 — Adenylyltransferase

结构域编号 domain_id	d1s4mb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamily	b.43.5 — Riboflavin kinase-like
家族 Family family	b.43.5.1 — ATP-dependent riboflavin kinase-like

结构域编号 domain_id	d1s4mb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
家族 Family family	c.26.1.3 — Adenylyltransferase

CATH v4.4 (4 domains)

结构域编号 domain_id	1s4mA01
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	620 — HUPs

结构域编号 domain_id	1s4mA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	30 — Riboflavin kinase-like

结构域编号 domain_id	1s4mB01
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	620 — HUPs

结构域编号 domain_id	1s4mB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	30 — Riboflavin kinase-like

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7. 引用文献 (1)

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晶胞边长 a length_a	66.093 Å
晶胞边长 b length_b	82.163 Å
晶胞边长 c length_c	66.754 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	116.57 °
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	2.100 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2230
R_work r_work	0.2120
R_free r_free	0.2587

fit	/app/data/saxs_computation/s4/1s4m/1s4m.fit
pddf	/app/data/pr_computation/s4/1s4m/1s4m.pr.out
profile	/app/data/saxs_computation/s4/1s4m/1s4m.dat

Crystal structure of flavin binding to FAD synthetase from Thermotoga maritina

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