1kyq

Met8p: A bifunctional NAD-dependent dehydrogenase and ferrochelatase involved in siroheme synthesis.

Method: X-RAY DIFFRACTION D_max: 100.1 Å Quality: EXCELLENT

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	1kyq
沉积日期 deposition_date	2002-02-05
结构标题 title	Met8p: A bifunctional NAD-dependent dehydrogenase and ferrochelatase involved in siroheme synthesis.
关键词 keywords	homodimer, OXIDOREDUCTASE, LYASE; OXIDOREDUCTASE, LYASE
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	32.59 Å
回转半径 Rg (电子) rg_electron	31.68 Å
零角强度 I(0) i0	147348000.00
分子量 molecular_weight	95261.0 kDa
排除体积 excluded_volume	118540 Å³
包络体积 envelope_volume	157620 Å³
水化壳体积 shell_volume	41649 Å³
包络直径 envelope_diameter	104.8 Å
壳层 Rg shell_rg	38.48 Å
包络 Rg envelope_rg	31.20 Å
形状 Rg shape_rg	31.68 Å
总 Rg total_rg	32.26 Å
总原子数 total_atoms	6628
残基数 n_residues	779
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	100.1 Å
Rg (实空间) rg_real	32.39 Å
Rg 误差 (实空间) rg_real_error	0.69 Å
I(0) (实空间) i0_real	1.4730e+08
I(0) 误差 (实空间) i0_real_error	2.2720e+06
Rg (倒空间) rg_reciprocal	32.48 Å
I(0) (倒空间) i0_reciprocal	147400000.0000
解质量估计 total_estimate	0.9085
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	42.9 Å
偏度 Skewness skewness	0.107
峰度 Kurtosis kurtosis	-0.553
角度范围 angular_range	— – 0.2450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	17650000.0000
实空间数据点数 n_real_points	50
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.947

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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	Siroheme biosynthesis protein MET8
分子量 formula_weight	32289.3 kDa
EC 编号 ec_number	1.-.-.-, 4.99.1.1
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	7289

MVKSLQLAHQLKDKRILLIGGGEVGLTRLYKLMPTGCKLTLVSPDLHKSIIPKFGKFIQNKDQPDYREDAKRFINPNWDPTKNEIYEYIRSDFKDEYLDLENENDAWYIIMTCIPDHPESARIYHLCKERFGKQQLVNVADKPDLCDFYFGANLEIGDRLQILISTNGLSPRFGALVRDEIRNLFTQMGDLALEDAVVKLGELRRGIRLLAPDDKDVKYRMDWARRCTDLFGIQHCHNIDVKRLLDLFKVMFQEQNCSLQFPPRERLLSEYCSS

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	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	614

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6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1kyqa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.11 — Siroheme synthase N-terminal domain-like

结构域编号 domain_id	d1kyqa2
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.37 — Siroheme synthase middle domains-like
超家族 Superfamily superfamily	e.37.1 — Siroheme synthase middle domains-like
家族 Family family	e.37.1.1 — Siroheme synthase middle domains-like

结构域编号 domain_id	d1kyqb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.11 — Siroheme synthase N-terminal domain-like

结构域编号 domain_id	d1kyqb2
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.37 — Siroheme synthase middle domains-like
超家族 Superfamily superfamily	e.37.1 — Siroheme synthase middle domains-like
家族 Family family	e.37.1.1 — Siroheme synthase middle domains-like

结构域编号 domain_id	d1kyqc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.11 — Siroheme synthase N-terminal domain-like

结构域编号 domain_id	d1kyqc2
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.37 — Siroheme synthase middle domains-like
超家族 Superfamily superfamily	e.37.1 — Siroheme synthase middle domains-like
家族 Family family	e.37.1.1 — Siroheme synthase middle domains-like

CATH v4.4 (9 domains)

结构域编号 domain_id	1kyqA01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1kyqA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	110 — Sirohaem synthase, central domain

结构域编号 domain_id	1kyqA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3280 — Siro heme synthase C-terminal domain-like
同源超家族 H-superfamily homologous superfamily	10 — Siroheme synthase; domain 3

结构域编号 domain_id	1kyqB01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1kyqB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	110 — Sirohaem synthase, central domain

结构域编号 domain_id	1kyqB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3280 — Siro heme synthase C-terminal domain-like
同源超家族 H-superfamily homologous superfamily	10 — Siroheme synthase; domain 3

结构域编号 domain_id	1kyqC01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1kyqC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	110 — Sirohaem synthase, central domain

结构域编号 domain_id	1kyqC03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3280 — Siro heme synthase C-terminal domain-like
同源超家族 H-superfamily homologous superfamily	10 — Siroheme synthase; domain 3

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7. 引用文献 (2)

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晶胞边长 a length_a	156.988 Å
晶胞边长 b length_b	80.856 Å
晶胞边长 c length_c	103.975 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	121.88 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

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	2.200 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2200
R_work r_work	0.2190
R_free r_free	0.2830

fit	/app/data/saxs_computation/ky/1kyq/1kyq.fit
pddf	/app/data/pr_computation/ky/1kyq/1kyq.pr.out
profile	/app/data/saxs_computation/ky/1kyq/1kyq.dat