2gbw

Crystal Structure of Biphenyl 2,3-Dioxygenase from Sphingomonas yanoikuyae B1

Method: X-RAY DIFFRACTION D_max: 111.3 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	2gbw
沉积日期 deposition_date	2006-03-12
结构标题 title	Crystal Structure of Biphenyl 2,3-Dioxygenase from Sphingomonas yanoikuyae B1
关键词 keywords	RIESKE OXYGENASE, OXIDOREDUCTASE, NON HEME IRON, DIOXYGENASE; 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	36.81 Å
回转半径 Rg (电子) rg_electron	35.84 Å
零角强度 I(0) i0	714584000.00
分子量 molecular_weight	212850.0 kDa
排除体积 excluded_volume	263450 Å³
包络体积 envelope_volume	317050 Å³
水化壳体积 shell_volume	69236 Å³
包络直径 envelope_diameter	119.2 Å
壳层 Rg shell_rg	45.20 Å
包络 Rg envelope_rg	35.75 Å
形状 Rg shape_rg	35.87 Å
总 Rg total_rg	36.28 Å
总原子数 total_atoms	15008
残基数 n_residues	1854
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	111.3 Å
Rg (实空间) rg_real	36.54 Å
Rg 误差 (实空间) rg_real_error	0.60 Å
I(0) (实空间) i0_real	7.1460e+08
I(0) 误差 (实空间) i0_real_error	1.1390e+07
Rg (倒空间) rg_reciprocal	36.71 Å
I(0) (倒空间) i0_reciprocal	714700000.0000
解质量估计 total_estimate	0.9027
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	49.2 Å
偏度 Skewness skewness	0.066
峰度 Kurtosis kurtosis	-0.585
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	245300000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.929

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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 (6)

Entity 1 polymer

描述 description	Biphenyl 2,3-Dioxygenase Alpha Subunit
分子量 formula_weight	51036.9 kDa
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	17030

MSSDATLVDTVNASQSRQVFWDEDVYALEIERIFSRAWLMLGHESLVPKPGDFITTYMAEDKVILSHQSDGTFRAFINSCSHRGNQICHADSGNAKAFVCNYHGWVFGQDGSLVDVPLESRCYHNSLDKQKLAAKSVRVETYKGFIFGCHDPEAPSLEDYLGEFRYYLDTIWEGAGGGMELLGPPMKSLLQCNWKVPAENFIGDGYHVGWTHAAALSQIGGELAGLAGNRADIPFDDLGLQFTTRHGHGFGVIDNAAAGLHIKREGWTKFLEDTRGEVRRKFGPERERLYLGHWNCSIFPNCSFLYGTNTFKIWHPRGPHEIEVWTYTIVPRDADPATKSMIQREAIRTFGTAGTLESDDGENMSSATYINRGVITRNGRMNSTMGVGYEGPHPVYPGIVGISFIGETSYRGFYRFWKEMIDAPDWASVKANDDTWDSVFPNRNFWNEKLNAAE

来源 Source

来源生物 organism	Sphingobium yanoikuyae
NCBI 分类编号 ncbi_taxonomy_id	13690
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	Biphenyl 2,3-Dioxygenase Beta Subunit
分子量 formula_weight	20786.3 kDa
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

MSSEQIPVTPDVHYDIEAHYRAEVRMFQTGQYREWLQGMVAEDIHYWMPIYEQRLTRDRRPDPTPDDAAIYNDDFGELKQRVERLYSGQVWMEDPPSKIRYFVSNVEAFEAGNGELDVLSNILVYRNRRQTEVTVHTLGREDKLRRDGNGFKVFRRKLILDARVTQDKNLYFFC

来源 Source

来源生物 organism	Sphingobium yanoikuyae
NCBI 分类编号 ncbi_taxonomy_id	13690
宿主生物 host_organism	Escherichia coli BL21(DE3)

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 non-polymer

描述 description	OXYGEN MOLECULE
分子量 formula_weight	32.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 6 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	1978

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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	d2gbwa1
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.33.1.0 — automated matches

结构域编号 domain_id	d2gbwa2
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.129.3.0 — automated matches

结构域编号 domain_id	d2gbwb_
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.17.4.0 — automated matches

结构域编号 domain_id	d2gbwc1
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.33.1.0 — automated matches

结构域编号 domain_id	d2gbwc2
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.129.3.0 — automated matches

结构域编号 domain_id	d2gbwd_
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.17.4.0 — automated matches

结构域编号 domain_id	d2gbwe1
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.33.1.0 — automated matches

结构域编号 domain_id	d2gbwe2
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.129.3.0 — automated matches

结构域编号 domain_id	d2gbwf_
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.17.4.0 — automated matches

CATH v4.4 (9 domains)

结构域编号 domain_id	2gbwA01
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	2gbwA02
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	2gbwB00
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	2gbwC01
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	2gbwC02
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	2gbwD00
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	2gbwE01
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	2gbwE02
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	2gbwF00
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	134.958 Å
晶胞边长 b length_b	134.958 Å
晶胞边长 c length_c	219.887 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	120.00 °
晶胞分子数 Z z_pdb	18

空间群 space_group	P 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	—

分辨率 resolution	1.700 Å
最低分辨率 resolution_low	19.800 Å
R 因子 r_factor	0.1901
R_work r_work	0.1881
R_free r_free	0.2283

fit	/app/data/saxs_computation/gb/2gbw/2gbw.fit
pddf	/app/data/pr_computation/gb/2gbw/2gbw.pr.out
profile	/app/data/saxs_computation/gb/2gbw/2gbw.dat

Crystal Structure of Biphenyl 2,3-Dioxygenase from Sphingomonas yanoikuyae B1

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 (6)

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 non-polymer

Entity 6 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)