1ndo

NAPHTHALENE 1,2-DIOXYGENASE

Method: X-RAY DIFFRACTION D_max: 105.1 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	1ndo
沉积日期 deposition_date	1998-01-11
结构标题 title	NAPHTHALENE 1,2-DIOXYGENASE
关键词 keywords	NON-HEME IRON DIOXYGENASE; NON-HEME IRON DIOXYGENASE
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	36.27 Å
回转半径 Rg (电子) rg_electron	35.31 Å
零角强度 I(0) i0	741719000.00
分子量 molecular_weight	216820.0 kDa
排除体积 excluded_volume	268700 Å³
包络体积 envelope_volume	322020 Å³
水化壳体积 shell_volume	70782 Å³
包络直径 envelope_diameter	113.0 Å
壳层 Rg shell_rg	45.19 Å
包络 Rg envelope_rg	35.16 Å
形状 Rg shape_rg	35.30 Å
总 Rg total_rg	35.92 Å
总原子数 total_atoms	15265
残基数 n_residues	1918
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	105.1 Å
Rg (实空间) rg_real	35.97 Å
Rg 误差 (实空间) rg_real_error	0.37 Å
I(0) (实空间) i0_real	7.4170e+08
I(0) 误差 (实空间) i0_real_error	1.0760e+07
Rg (倒空间) rg_reciprocal	36.16 Å
I(0) (倒空间) i0_reciprocal	741800000.0000
解质量估计 total_estimate	0.8974
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	47.8 Å
偏度 Skewness skewness	0.021
峰度 Kurtosis kurtosis	-0.594
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	283600000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.810

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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	NAPHTHALENE 1,2-DIOXYGENASE
分子量 formula_weight	49664.4 kDa
EC 编号 ec_number	1.14.12.12
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,C,E
原子数 atom_count	16326

MNYNNKILVSESGLSQKHLIHGDEELFQHELKTIFARNWLFLTHDSLIPAPGDYVTAKMGIDEVIVSRQNDGSIRAFLNVCRHRGKTLVSVEAGNAKGFVCSYHGWGFGSNGELQSVPFEKDLYGESLNKKCLGLKEVARVESFHGFIYGCFDQEAPPLMDYLGDAAWYLEPMFKHSGGLELVGPPGKVVIKANWKAPAENFVGDAYHVGWTHASSLRSGESIFSSLAGNAALPPEGAGLQMTSKYGSGMGVLWDGYSGVHSADLVPELMAFGGAKQERLNKEIGDVRARIYRSHLNCTVFPNNSMLTCSGVFKVWNPIDANTTEVWTYAIVEKDMPEDLKRRLADSVQRTFGPAGFWESDDNDNMETASQNGKKYQSRDSDLLSNLGFGEDVYGDAVYPGVVGKSAIGETSYRGFYRAYQAHVSSSNWAEFEHASSTWHTELTKTTDR

来源 Source

来源生物 organism	Pseudomonas putida
NCBI 分类编号 ncbi_taxonomy_id	303
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	NAPHTHALENE 1,2-DIOXYGENASE
分子量 formula_weight	22969.1 kDa
EC 编号 ec_number	1.14.12.12
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	B,D,F

MMINIQEDKLVSAHDAEEILRFFNCHDSALQQEATTLLTQEAHLLDIQAYRAWLEHCVGSEVQYQVISRELRAASERRYKLNEAMNVYNENFQQLKVRVEHQLDPQNWGNSPKLRFTRFITNVQAAMDVNDKELLHIRSNVILHRARRGNQVDVFYAAREDKWKRGEGGVRKLVQRFVDYPERILQTHNLMVFL

来源 Source

来源生物 organism	Pseudomonas putida
NCBI 分类编号 ncbi_taxonomy_id	303
宿主生物 host_organism	Escherichia coli

Entity 3 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	3

Entity 4 non-polymer

描述 description	FE2/S2 (INORGANIC) CLUSTER
分子量 formula_weight	175.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	1061

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

结构域编号 domain_id	d1ndoa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.33 — ISP domain
超家族 Superfamily superfamily	b.33.1 — ISP domain
家族 Family family	b.33.1.2 — Ring hydroxylating alpha subunit ISP domain

结构域编号 domain_id	d1ndoa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.129 — TBP-like
超家族 Superfamily superfamily	d.129.3 — Bet v1-like
家族 Family family	d.129.3.3 — Ring hydroxylating alpha subunit catalytic domain

结构域编号 domain_id	d1ndob_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.4 — Ring hydroxylating beta subunit

结构域编号 domain_id	d1ndoc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.33 — ISP domain
超家族 Superfamily superfamily	b.33.1 — ISP domain
家族 Family family	b.33.1.2 — Ring hydroxylating alpha subunit ISP domain

结构域编号 domain_id	d1ndoc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.129 — TBP-like
超家族 Superfamily superfamily	d.129.3 — Bet v1-like
家族 Family family	d.129.3.3 — Ring hydroxylating alpha subunit catalytic domain

结构域编号 domain_id	d1ndod_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.4 — Ring hydroxylating beta subunit

结构域编号 domain_id	d1ndoe1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.33 — ISP domain
超家族 Superfamily superfamily	b.33.1 — ISP domain
家族 Family family	b.33.1.2 — Ring hydroxylating alpha subunit ISP domain

结构域编号 domain_id	d1ndoe2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.129 — TBP-like
超家族 Superfamily superfamily	d.129.3 — Bet v1-like
家族 Family family	d.129.3.3 — Ring hydroxylating alpha subunit catalytic domain

结构域编号 domain_id	d1ndof_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.4 — Ring hydroxylating beta subunit

CATH v4.4 (9 domains)

结构域编号 domain_id	1ndoA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	380 — Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1

结构域编号 domain_id	1ndoA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	102 — 3-layer Sandwich
拓扑 Topology topology	10 — Rieske Iron-sulfur Protein
同源超家族 H-superfamily homologous superfamily	10 — Rieske [2Fe-2S] iron-sulphur domain

结构域编号 domain_id	1ndoB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1ndoC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	380 — Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1

结构域编号 domain_id	1ndoC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	102 — 3-layer Sandwich
拓扑 Topology topology	10 — Rieske Iron-sulfur Protein
同源超家族 H-superfamily homologous superfamily	10 — Rieske [2Fe-2S] iron-sulphur domain

结构域编号 domain_id	1ndoD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1ndoE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	380 — Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1

结构域编号 domain_id	1ndoE02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	102 — 3-layer Sandwich
拓扑 Topology topology	10 — Rieske Iron-sulfur Protein
同源超家族 H-superfamily homologous superfamily	10 — Rieske [2Fe-2S] iron-sulphur domain

结构域编号 domain_id	1ndoF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

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7. 引用文献 (1)

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晶胞边长 a length_a	105.000 Å
晶胞边长 b length_b	174.000 Å
晶胞边长 c length_c	282.500 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	24

空间群 space_group	I 2 2 2
空间群编号 int_tables_number	23
晶系 crystal_system	—

分辨率 resolution	2.250 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2200
R_work r_work	0.1900
R_free r_free	0.2400

fit	/app/data/saxs_computation/nd/1ndo/1ndo.fit
pddf	/app/data/pr_computation/nd/1ndo/1ndo.pr.out
profile	/app/data/saxs_computation/nd/1ndo/1ndo.dat

NAPHTHALENE 1,2-DIOXYGENASE

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 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)