SAXSdb — 2gep

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2gep
沉积日期 deposition_date	1997-07-10
结构标题 title	SULFITE REDUCTASE HEMOPROTEIN, OXIDIZED, SIROHEME FEIII [4FE-4S] +2,SULFITE COMPLEX
关键词 keywords	OXIDOREDUCTASE, SIROHEME FEIII, [4FE-4S], SULFITE COMPLEX; 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	22.37 Å
回转半径 Rg (电子) rg_electron	21.57 Å
零角强度 I(0) i0	49185900.00
分子量 molecular_weight	54091.0 kDa
排除体积 excluded_volume	67499 Å³
包络体积 envelope_volume	75222 Å³
水化壳体积 shell_volume	27910 Å³
包络直径 envelope_diameter	67.5 Å
壳层 Rg shell_rg	29.31 Å
包络 Rg envelope_rg	21.85 Å
形状 Rg shape_rg	21.60 Å
总 Rg total_rg	22.32 Å
总原子数 total_atoms	3788
残基数 n_residues	472
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	67.1 Å
Rg (实空间) rg_real	22.22 Å
Rg 误差 (实空间) rg_real_error	0.34 Å
I(0) (实空间) i0_real	4.9190e+07
I(0) 误差 (实空间) i0_real_error	6.1950e+05
Rg (倒空间) rg_reciprocal	22.26 Å
I(0) (倒空间) i0_reciprocal	49190000.0000
解质量估计 total_estimate	0.7513
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	28.5 Å
偏度 Skewness skewness	0.109
峰度 Kurtosis kurtosis	-0.541
角度范围 angular_range	— – 0.3550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	10170000.0000
实空间数据点数 n_real_points	67
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 0.328; Positv: 1.000; Valcen: 0.981; Smooth: 0.968

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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 (6)

Entity 1 polymer

描述 description	SULFITE REDUCTASE HEMOPROTEIN
分子量 formula_weight	55747.7 kDa
EC 编号 ec_number	1.8.1.2
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	4138

LEPRHAMLLRCRLPGGVITTKQWQAIDKFAGENTIYGSIRLTNRQTFQFHGILKKNVKPVHQMLHSVGLDALATANDMNRNVLCTSNPYESQLHAEAYEWAKKISEHLLPRTRAYAEIWLDQEKVATTDEEPILGQTYLPRKFKTTVVIPPQNDIDLHANDMNFVAIAENGKLVGFNLLVGGGLSIEHGNKKTYARTASEFGYLPLEHTLAVAEAVVTTQRDWGNRTDRKNAKTKYTLERVGVETFKAEVERRAGIKFEPIRPYEFTGRGDRIGWVKGIDDNWHLTLFIENGRILDYPARPLKTGLLEIAKIHKGDFRITANQNLIIAGVPESEKAKIEKIAKESGLMNAVTPQRENSMACVSFPTCPLAMAEAERFLPSFIDNIDNLMAKHGVSDEHIVMRVTGCPNGCGRAMLAEVGLVGKAPGRYNLHLGGNRIGTRIPRMYKENITEPEILASLDELIGRWAKEREAGEGFGDFTVRAGIIRPVLDPARDLWD

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	37762
宿主生物 host_organism	Salmonella typhimurium

Entity 2 non-polymer

描述 description	SULFITE ION
分子量 formula_weight	80.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	SIROHEME
分子量 formula_weight	916.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 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	350

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6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2gepa1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.36 — Nitrite/Sulfite reductase N-terminal domain-like
家族 Family family	d.58.36.1 — Duplicated SiR/NiR-like domains 1 and 3

结构域编号 domain_id	d2gepa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.36 — Nitrite/Sulfite reductase N-terminal domain-like
家族 Family family	d.58.36.1 — Duplicated SiR/NiR-like domains 1 and 3

结构域编号 domain_id	d2gepa3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.134 — Nitrite and sulphite reductase 4Fe-4S domain-like
超家族 Superfamily superfamily	d.134.1 — Nitrite and sulphite reductase 4Fe-4S domain-like
家族 Family family	d.134.1.1 — Nitrite and sulphite reductase 4Fe-4S domain-like

结构域编号 domain_id	d2gepa4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.134 — Nitrite and sulphite reductase 4Fe-4S domain-like
超家族 Superfamily superfamily	d.134.1 — Nitrite and sulphite reductase 4Fe-4S domain-like
家族 Family family	d.134.1.1 — Nitrite and sulphite reductase 4Fe-4S domain-like

CATH v4.4 (3 domains)

结构域编号 domain_id	2gepA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	413 — Sulfite Reductase Hemoprotein; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Sulfite Reductase Hemoprotein, domain 1

结构域编号 domain_id	2gepA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	480 — Sulfite Reductase Hemoprotein; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Sulfite Reductase Hemoprotein;Domain 2

结构域编号 domain_id	2gepA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	413 — Sulfite Reductase Hemoprotein; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Sulfite Reductase Hemoprotein, domain 1

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7. 引用文献 (2)

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晶胞边长 a length_a	69.800 Å
晶胞边长 b length_b	77.400 Å
晶胞边长 c length_c	87.800 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	4

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.1750
R_work r_work	0.1750
R_free r_free	—

fit	/app/data/saxs_computation/ge/2gep/2gep.fit
pddf	/app/data/pr_computation/ge/2gep/2gep.pr.out
profile	/app/data/saxs_computation/ge/2gep/2gep.dat

SULFITE REDUCTASE HEMOPROTEIN, OXIDIZED, SIROHEME FEIII [4FE-4S] +2,SULFITE COMPLEX

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution