1tlb

Yeast coproporphyrinogen oxidase

Method: X-RAY DIFFRACTION D_max: 135.8 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1tlb
沉积日期 deposition_date	2004-06-09
结构标题 title	Yeast coproporphyrinogen oxidase
关键词 keywords	coproporphyrinogen oxidase, heme biosynthesis, enzyme, 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	44.92 Å
回转半径 Rg (电子) rg_electron	44.45 Å
零角强度 I(0) i0	750969000.00
分子量 molecular_weight	224840.0 kDa
排除体积 excluded_volume	280090 Å³
包络体积 envelope_volume	377540 Å³
水化壳体积 shell_volume	68862 Å³
包络直径 envelope_diameter	136.5 Å
壳层 Rg shell_rg	51.22 Å
包络 Rg envelope_rg	43.54 Å
形状 Rg shape_rg	44.43 Å
总 Rg total_rg	44.78 Å
总原子数 total_atoms	15891
残基数 n_residues	1956
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	135.8 Å
Rg (实空间) rg_real	44.73 Å
Rg 误差 (实空间) rg_real_error	0.95 Å
I(0) (实空间) i0_real	7.5100e+08
I(0) 误差 (实空间) i0_real_error	1.2620e+07
Rg (倒空间) rg_reciprocal	44.92 Å
I(0) (倒空间) i0_reciprocal	751100000.0000
解质量估计 total_estimate	0.8963
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	54.3 Å
偏度 Skewness skewness	0.050
峰度 Kurtosis kurtosis	-0.807
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	62940000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.972; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.732

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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	Coproporphyrinogen III oxidase
分子量 formula_weight	37535.2 kDa
EC 编号 ec_number	1.3.3.3
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,D,Q,S,U,W
原子数 atom_count	16531

APQDPRNLPIRQQMEALIRRKQAEITQGLESIDTVKFHADTWTRGNDGGGGTSMVIQDGTTFEKGGVNVSVVYGQLSPAAVSAMKADHKNLRLPEDPKTGLPVTDGVKFFACGLSMVIHPVNPHAPTTHLNYRYFETWNQDGTPQTWWFGGGADLTPSYLYEEDGQLFHQLHKDALDKHDTALYPRFKKWCDEYFYITHRKETRGIGGIFFDDYDERDPQEILKMVEDCFDAFLPSYLTIVKRRKDMPYTKEEQQWQAIRRGRYVEFNLIYDRGTQFGLRTPGSRVESILMSLPEHASWLYNHHPAPGSREAKLLEVTTKPREWVK

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 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	640

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1tlba_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.248 — Coproporphyrinogen III oxidase
超家族 Superfamily superfamily	d.248.1 — Coproporphyrinogen III oxidase
家族 Family family	d.248.1.1 — Coproporphyrinogen III oxidase

结构域编号 domain_id	d1tlbd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.248 — Coproporphyrinogen III oxidase
超家族 Superfamily superfamily	d.248.1 — Coproporphyrinogen III oxidase
家族 Family family	d.248.1.1 — Coproporphyrinogen III oxidase

结构域编号 domain_id	d1tlbq_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.248 — Coproporphyrinogen III oxidase
超家族 Superfamily superfamily	d.248.1 — Coproporphyrinogen III oxidase
家族 Family family	d.248.1.1 — Coproporphyrinogen III oxidase

结构域编号 domain_id	d1tlbs_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.248 — Coproporphyrinogen III oxidase
超家族 Superfamily superfamily	d.248.1 — Coproporphyrinogen III oxidase
家族 Family family	d.248.1.1 — Coproporphyrinogen III oxidase

结构域编号 domain_id	d1tlbu_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.248 — Coproporphyrinogen III oxidase
超家族 Superfamily superfamily	d.248.1 — Coproporphyrinogen III oxidase
家族 Family family	d.248.1.1 — Coproporphyrinogen III oxidase

结构域编号 domain_id	d1tlbw_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.248 — Coproporphyrinogen III oxidase
超家族 Superfamily superfamily	d.248.1 — Coproporphyrinogen III oxidase
家族 Family family	d.248.1.1 — Coproporphyrinogen III oxidase

CATH v4.4 (6 domains)

结构域编号 domain_id	1tlbA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1500 — oxygen-dependent coproporphyrinogen oxidase
同源超家族 H-superfamily homologous superfamily	10 — Coproporphyrinogen III oxidase, aerobic

结构域编号 domain_id	1tlbD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1500 — oxygen-dependent coproporphyrinogen oxidase
同源超家族 H-superfamily homologous superfamily	10 — Coproporphyrinogen III oxidase, aerobic

结构域编号 domain_id	1tlbQ00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1500 — oxygen-dependent coproporphyrinogen oxidase
同源超家族 H-superfamily homologous superfamily	10 — Coproporphyrinogen III oxidase, aerobic

结构域编号 domain_id	1tlbS00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1500 — oxygen-dependent coproporphyrinogen oxidase
同源超家族 H-superfamily homologous superfamily	10 — Coproporphyrinogen III oxidase, aerobic

结构域编号 domain_id	1tlbU00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1500 — oxygen-dependent coproporphyrinogen oxidase
同源超家族 H-superfamily homologous superfamily	10 — Coproporphyrinogen III oxidase, aerobic

结构域编号 domain_id	1tlbW00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1500 — oxygen-dependent coproporphyrinogen oxidase
同源超家族 H-superfamily homologous superfamily	10 — Coproporphyrinogen III oxidase, aerobic

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7. 引用文献 (1)

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晶胞边长 a length_a	232.773 Å
晶胞边长 b length_b	65.238 Å
晶胞边长 c length_c	166.071 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	107.85 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	158.110 Å
R 因子 r_factor	0.2119
R_work r_work	0.2082
R_free r_free	0.2824

fit	/app/data/saxs_computation/tl/1tlb/1tlb.fit
pddf	/app/data/pr_computation/tl/1tlb/1tlb.pr.out
profile	/app/data/saxs_computation/tl/1tlb/1tlb.dat