2de5

Crystal structure of the electron transfer complex between oxygenase and ferredoxin in carbazole 1,9a-dioxygenase

Method: X-RAY DIFFRACTION D_max: 120.8 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	2de5
沉积日期 deposition_date	2006-02-08
结构标题 title	Crystal structure of the electron transfer complex between oxygenase and ferredoxin in carbazole 1,9a-dioxygenase
关键词 keywords	;Electron transfer complex, Rieske non-heme iron oxygenase system, Terminal oxygenase, Rieske-type ferredoxin, carbazole 1, 9a-dioxygenase, 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	38.94 Å
回转半径 Rg (电子) rg_electron	38.22 Å
零角强度 I(0) i0	425233000.00
分子量 molecular_weight	167710.0 kDa
排除体积 excluded_volume	208920 Å³
包络体积 envelope_volume	266200 Å³
水化壳体积 shell_volume	55210 Å³
包络直径 envelope_diameter	130.8 Å
壳层 Rg shell_rg	46.89 Å
包络 Rg envelope_rg	37.96 Å
形状 Rg shape_rg	38.22 Å
总 Rg total_rg	38.68 Å
总原子数 total_atoms	11764
残基数 n_residues	1482
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	120.8 Å
Rg (实空间) rg_real	38.67 Å
Rg 误差 (实空间) rg_real_error	0.69 Å
I(0) (实空间) i0_real	4.2520e+08
I(0) 误差 (实空间) i0_real_error	5.9690e+06
Rg (倒空间) rg_reciprocal	38.84 Å
I(0) (倒空间) i0_reciprocal	425300000.0000
解质量估计 total_estimate	0.8997
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	56.0 Å
偏度 Skewness skewness	0.015
峰度 Kurtosis kurtosis	-0.665
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	73070000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.941

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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	terminal oxygenase component of carbazole
分子量 formula_weight	44910.7 kDa
EC 编号 ec_number	1.14.12.-
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,B,C
原子数 atom_count	12842

MANVDEAILKRVKGWAPYVDAKLGFRNHWYPVMFSKEINEGEPKTLKLLGENLLVNRIDGKLYCLKDRCLHRGVQLSVKVECKTKSTITCWYHAWTYRWEDGVLCDILTNPTSAQIGRQKLKTYPVQEAKGCVFIYLGDGDPPPLARDTPPNFLDDDMEILGKNQIIKSNWRLAVENGFDPSHIYIHKDSILVKDNDLALPLGFAPGGDRKQQTRVVDDDVVGRKGVYDLIGEHGVPVFEGTIGGEVVREGAYGEKIVANDISIWLPGVLKVNPFPNPDMMQFEWYVPIDENTHYYFQTLGKPCANDEERKKYEQEFESKWKPMALEGFNNDDIWAREAMVDFYADDKGWVNEILFESDEAIVAWRKLASEHNQGIQTQAHVSGLEHHHHHH

来源 Source

来源生物 organism	Janthinobacterium
NCBI 分类编号 ncbi_taxonomy_id	29580
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	ferredoxin component of carbazole
分子量 formula_weight	12448.1 kDa
EC 编号 ec_number	1.14.12.-
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	D,E,F

MNQIWLKVCAASDMQPGTIRRVNRVGAAPLAVYRVGDQFYATEDTCTHGIASLSEGTLDGDVIECPFHGGAFNVCTGMPASSPCTVPLGVFEVEVKEGEVYVAGEKKLEHHHHHH

来源 Source

来源生物 organism	Pseudomonas resinovorans
NCBI 分类编号 ncbi_taxonomy_id	53412
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

描述 description	FE (II) 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	6

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	1078

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6. 折叠分类 (SCOP + CATH) 21 domains

SCOP 2.08 (9 domains)

结构域编号 domain_id	d2de5a1
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	d2de5a2
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	d2de5a3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2de5b1
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	d2de5b2
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	d2de5b3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2de5c1
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	d2de5c2
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	d2de5c3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (12 domains)

结构域编号 domain_id	2de5A01
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	2de5A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily	680 —

结构域编号 domain_id	2de5A03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2de5B01
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	2de5B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily	680 —

结构域编号 domain_id	2de5B03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2de5C01
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	2de5C02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily	680 —

结构域编号 domain_id	2de5C03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2de5D00
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	2de5E00
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	2de5F00
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

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7. 引用文献 (1)

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晶胞边长 a length_a	98.091 Å
晶胞边长 b length_b	89.835 Å
晶胞边长 c length_c	104.914 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	103.79 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	6

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	1.900 Å
最低分辨率 resolution_low	44.920 Å
R 因子 r_factor	0.1990
R_work r_work	0.1990
R_free r_free	0.2330

fit	/app/data/saxs_computation/de/2de5/2de5.fit
pddf	/app/data/pr_computation/de/2de5/2de5.pr.out
profile	/app/data/saxs_computation/de/2de5/2de5.dat

Crystal structure of the electron transfer complex between oxygenase and ferredoxin in carbazole 1,9a-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) 21 domains

SCOP 2.08 (9 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)