1pn0

Phenol hydroxylase from Trichosporon cutaneum

Method: X-RAY DIFFRACTION D_max: 143.0 Å Quality: REASONABLE

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	1pn0
沉积日期 deposition_date	2003-06-12
结构标题 title	Phenol hydroxylase from Trichosporon cutaneum
关键词 keywords	two dimers, TLS refinement, 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	44.73 Å
回转半径 Rg (电子) rg_electron	44.29 Å
零角强度 I(0) i0	1373060000.00
分子量 molecular_weight	299620.0 kDa
排除体积 excluded_volume	371440 Å³
包络体积 envelope_volume	477230 Å³
水化壳体积 shell_volume	86122 Å³
包络直径 envelope_diameter	155.5 Å
壳层 Rg shell_rg	52.08 Å
包络 Rg envelope_rg	43.68 Å
形状 Rg shape_rg	44.27 Å
总 Rg total_rg	44.66 Å
总原子数 total_atoms	21084
残基数 n_residues	2616
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	143.0 Å
Rg (实空间) rg_real	44.55 Å
Rg 误差 (实空间) rg_real_error	0.88 Å
I(0) (实空间) i0_real	1.3730e+09
I(0) 误差 (实空间) i0_real_error	2.3410e+07
Rg (倒空间) rg_reciprocal	44.73 Å
I(0) (倒空间) i0_reciprocal	1373000000.0000
解质量估计 total_estimate	0.6588
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	57.2 Å
偏度 Skewness skewness	0.214
峰度 Kurtosis kurtosis	-0.383
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	140600000.0000
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: 0.899; Stabil: 1.000; Sysdev: 0.010; Positv: 1.000; Valcen: 0.993; Smooth: 0.841

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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	Phenol 2-monooxygenase
分子量 formula_weight	75313.9 kDa
EC 编号 ec_number	1.14.13.7
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	23772

MTKYSESYCDVLIVGAGPAGLMAARVLSEYVRQKPDLKVRIIDKRSTKVYNGQADGLQCRTLESLKNLGLADKILSEANDMSTIALYNPDENGHIRRTDRIPDTLPGISRYHQVVLHQGRIERRILDSIAEISDTRIKVERPLIPEKMEIDSSKAEDPEAYPVTMTLRYMSEDESTPLQFGHKTENGLFRSNLQTQEEEDANYRLPEGKEAGEIETVHCKYVIGCDGGHSWVRRTLGFEMIGEQTDYIWGVLDAVPASNFPDIRSRCAIHSAESGSIMIIPRENNLVRFYVQLQARAEKGGRVDRTKFTPEVVIANAKKIFHPYTFDVQQLDWFTAYHIGQRVTEKFSKDERVFIAGDACHTHSPKAGQGMNTSMMDTYNLGWKLGLVLTGRAKRDILKTYEEERQPFAQALIDFDHQFSRLFSGRPAKDVADEMGVSMDVFKEAFVKGNEFASGTAINYDENLVTDKKSSKQELAKNCVVGTRFKSQPVVRHSEGLWMHFGDRLVTDGRFRIIVFAGKATDATQMSRIKKFAAYLDSENSVISRYTPKGADRNSRIDVITIHSCHRDDIEMHDFPAPALHPKWQYDFIYADCDSWHHPHPKSYQAWGVDETKGAVVVVRPDGYTSLVTDLEGTAEIDRYFSGILVEPKEKSGAQTEADWTKSTA

来源 Source

来源生物 organism	Trichosporon cutaneum
NCBI 分类编号 ncbi_taxonomy_id	5554
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	4

Entity 3 non-polymer

描述 description	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	PHENOL
分子量 formula_weight	94.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	2688

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1pn0a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d1pn0a2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.10 — Glutathione peroxidase-like

结构域编号 domain_id	d1pn0a3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.2 — PHBH-like

结构域编号 domain_id	d1pn0b1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d1pn0b2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.10 — Glutathione peroxidase-like

结构域编号 domain_id	d1pn0b3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.2 — PHBH-like

结构域编号 domain_id	d1pn0c1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d1pn0c2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.10 — Glutathione peroxidase-like

结构域编号 domain_id	d1pn0c3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.2 — PHBH-like

结构域编号 domain_id	d1pn0d1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d1pn0d2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.10 — Glutathione peroxidase-like

结构域编号 domain_id	d1pn0d3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.2 — PHBH-like

CATH v4.4 (12 domains)

结构域编号 domain_id	1pn0A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1pn0A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	9 — D-Amino Acid Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-Amino Acid Oxidase, subunit A, domain 2

结构域编号 domain_id	1pn0A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	20 — Phenol hydroxylase, C-terminal dimerisation domain

结构域编号 domain_id	1pn0B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1pn0B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	9 — D-Amino Acid Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-Amino Acid Oxidase, subunit A, domain 2

结构域编号 domain_id	1pn0B03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	20 — Phenol hydroxylase, C-terminal dimerisation domain

结构域编号 domain_id	1pn0C01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1pn0C02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	9 — D-Amino Acid Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-Amino Acid Oxidase, subunit A, domain 2

结构域编号 domain_id	1pn0C03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	20 — Phenol hydroxylase, C-terminal dimerisation domain

结构域编号 domain_id	1pn0D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1pn0D02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	9 — D-Amino Acid Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-Amino Acid Oxidase, subunit A, domain 2

结构域编号 domain_id	1pn0D03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	20 — Phenol hydroxylase, C-terminal dimerisation domain

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7. 引用文献 (2)

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晶胞边长 a length_a	99.999 Å
晶胞边长 b length_b	150.948 Å
晶胞边长 c length_c	114.962 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	114.63 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	1.700 Å
最低分辨率 resolution_low	19.960 Å
R 因子 r_factor	0.1570
R_work r_work	0.1570
R_free r_free	0.1799

fit	/app/data/saxs_computation/pn/1pn0/1pn0.fit
pddf	/app/data/pr_computation/pn/1pn0/1pn0.pr.out
profile	/app/data/saxs_computation/pn/1pn0/1pn0.dat