SAXSdb — 2inp

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2inp
沉积日期 deposition_date	2006-10-08
结构标题 title	Structure of the Phenol Hydroxylase-Regulatory Protein Complex
关键词 keywords	hydroxylase, diiron, four-helix bundle, regulatory protein, 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	40.92 Å
回转半径 Rg (电子) rg_electron	40.61 Å
零角强度 I(0) i0	763780000.00
分子量 molecular_weight	226450.0 kDa
排除体积 excluded_volume	281860 Å³
包络体积 envelope_volume	338710 Å³
水化壳体积 shell_volume	67700 Å³
包络直径 envelope_diameter	136.1 Å
壳层 Rg shell_rg	47.57 Å
包络 Rg envelope_rg	40.48 Å
形状 Rg shape_rg	40.61 Å
总 Rg total_rg	40.92 Å
总原子数 total_atoms	15957
残基数 n_residues	1952
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	134.0 Å
Rg (实空间) rg_real	40.88 Å
Rg 误差 (实空间) rg_real_error	0.91 Å
I(0) (实空间) i0_real	7.6380e+08
I(0) 误差 (实空间) i0_real_error	1.3240e+07
Rg (倒空间) rg_reciprocal	40.92 Å
I(0) (倒空间) i0_reciprocal	763800000.0000
解质量估计 total_estimate	0.8874
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	44.7 Å
偏度 Skewness skewness	0.287
峰度 Kurtosis kurtosis	-0.504
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	231600000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.831

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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 (7)

Entity 1 polymer

描述 description	Phenol hydroxylase component phN
分子量 formula_weight	58401.5 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	17022

KKLNLKDKYQYLTRDMAWEPTYQDKKDIFPEEDFEGIKITDWSQWEDPFRLTMDAYWKYQAEKEKKLYAIFDAFAQNNGHQNISDARYVNALKLFISGISPLEHAAFQGYSKVGRQFSGAGARVACQMQAIDELRHSQTQQHAMSHYNKHFNGLHDGPHMHDRVWYLSVPKSFFDDARSAGPFEFLTAISFSFEYVLTNLLFVPFMSGAAYNGDMATVTFGFSAQSDEARHMTLGLEVIKFILEQHEDNVPIVQRWIDKWFWRGFRLLSLVSMMMDYMLPNKVMSWSEAWEVYYEQNGGALFKDLERYGIRPPKYQDVANDAKHHLSHQLWTTFYQYCQATNFHTWIPEKEEMDWMSEKYPDTFDKYYRPRYEYLAKEAAAGRRFYNNTLPQLCQVCQIPTIFTEKDAPTMLSHRQIEHEGERYHFCSDGCCDIFKHEPEKYIQAWLPVHQIYQGNCEGGDLETVVQKYYHINIGEDNFDYVGSPDQKHWLSIK

来源 Source

来源生物 organism	Pseudomonas stutzeri
NCBI 分类编号 ncbi_taxonomy_id	316
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Phenol hydroxylase component phL
分子量 formula_weight	37968.8 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	C,D

EIKTNSVEPIRHTYGHIARRFGDKPATRYQEASYDIEAKTNFHYRPQWDSEHTLNDPTRTAIRMEDWCAVSDPRQFYYGAYVGNRAKMQESAETSFGFCEKRNLLTRLSEETQKQLLRLLVPLRHVELGANMNNAKIAGDATATTVSQMHIYTGMDRLGIGQYLSRIALMIDGSTGAALDESKAYWMDDEMWQPMRKLVEDTLVVDDWFELTLVQNILIDGMMYPLVYDKMDQWFESQGAEDVSMLTEFMRDWYKESLRWTNAMMKAVAGESETNRELLQKWIDHWEPQAYEALKPLAEASVGIDGLNEARAELSARLKKFELQSRGV

来源 Source

来源生物 organism	Pseudomonas stutzeri
NCBI 分类编号 ncbi_taxonomy_id	316
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	Phenol hydroxylase component phO
分子量 formula_weight	13116.9 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	E,F

SVNALYDYKFEPKDKVENFHGMQLLYVYWPDHLLFCAPFALLVQPGMTFSALVDEILKPATAAHPDSAKADFLNAEWLLNDEPFTPKADASLKEQGIDHKSMLTVTTPGLKGMANAGY

来源 Source

来源生物 organism	Pseudomonas stutzeri
NCBI 分类编号 ncbi_taxonomy_id	316
宿主生物 host_organism	Escherichia coli

Entity 4 polymer

描述 description	Phenol hydroxylase component phM
分子量 formula_weight	10488.7 kDa
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	L

MSQLVFIVFQDNDDSRYLAEAVMEDNPDAEMQHQPAMIRIQAEKRLVINRETMEEKLGRDWDVQEMLINVISIAGNVDEDDDHFILEWN

来源 Source

来源生物 organism	Pseudomonas stutzeri
NCBI 分类编号 ncbi_taxonomy_id	316
宿主生物 host_organism	Escherichia coli

Entity 5 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 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	1022

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d2inpl_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.137 — Monooxygenase (hydroxylase) regulatory protein
超家族 Superfamily superfamily	d.137.1 — Monooxygenase (hydroxylase) regulatory protein
家族 Family family	d.137.1.1 — Monooxygenase (hydroxylase) regulatory protein

CATH v4.4 (7 domains)

结构域编号 domain_id	2inpA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	620 — Ribonucleotide Reductase, subunit A
同源超家族 H-superfamily homologous superfamily	20 — Ribonucleotide Reductase, subunit A

结构域编号 domain_id	2inpB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	620 — Ribonucleotide Reductase, subunit A
同源超家族 H-superfamily homologous superfamily	20 — Ribonucleotide Reductase, subunit A

结构域编号 domain_id	2inpC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	620 — Ribonucleotide Reductase, subunit A
同源超家族 H-superfamily homologous superfamily	20 — Ribonucleotide Reductase, subunit A

结构域编号 domain_id	2inpD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	620 — Ribonucleotide Reductase, subunit A
同源超家族 H-superfamily homologous superfamily	20 — Ribonucleotide Reductase, subunit A

结构域编号 domain_id	2inpE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	560 — Phenol hydroxylase

结构域编号 domain_id	2inpF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	560 — Phenol hydroxylase

结构域编号 domain_id	2inpL00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	56 — Phenol Hydroxylase P2 Protein
同源超家族 H-superfamily homologous superfamily	10 — Monooxygenase component MmoB/DmpM

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7. 引用文献 (1)

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晶胞边长 a length_a	87.751 Å
晶胞边长 b length_b	146.305 Å
晶胞边长 c length_c	190.020 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	8

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	2.300 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.1980
R_work r_work	0.1920
R_free r_free	0.2360

fit	/app/data/saxs_computation/in/2inp/2inp.fit
pddf	/app/data/pr_computation/in/2inp/2inp.pr.out
profile	/app/data/saxs_computation/in/2inp/2inp.dat

Structure of the Phenol Hydroxylase-Regulatory Protein Complex

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

5. 实体与聚合体信息 (7)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (1 domains)

CATH v4.4 (7 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)