1ykp

Protocatechuate 3,4-Dioxygenase Y408H mutant bound to DHB

Method: X-RAY DIFFRACTION D_max: 157.9 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	1ykp
沉积日期 deposition_date	2005-01-18
结构标题 title	Protocatechuate 3,4-Dioxygenase Y408H mutant bound to DHB
关键词 keywords	protocatechuate, catechol, 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	48.41 Å
回转半径 Rg (电子) rg_electron	47.64 Å
零角强度 I(0) i0	1293050000.00
分子量 molecular_weight	293980.0 kDa
排除体积 excluded_volume	365130 Å³
包络体积 envelope_volume	499620 Å³
水化壳体积 shell_volume	84295 Å³
包络直径 envelope_diameter	160.2 Å
壳层 Rg shell_rg	55.01 Å
包络 Rg envelope_rg	46.44 Å
形状 Rg shape_rg	47.64 Å
总 Rg total_rg	47.87 Å
总原子数 total_atoms	20760
残基数 n_residues	2622
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	157.9 Å
Rg (实空间) rg_real	48.26 Å
Rg 误差 (实空间) rg_real_error	1.45 Å
I(0) (实空间) i0_real	1.2930e+09
I(0) 误差 (实空间) i0_real_error	2.7030e+07
Rg (倒空间) rg_reciprocal	48.41 Å
I(0) (倒空间) i0_reciprocal	1293000000.0000
解质量估计 total_estimate	0.9014
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	62.2 Å
偏度 Skewness skewness	0.169
峰度 Kurtosis kurtosis	-0.632
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	284400000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.946

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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	Protocatechuate 3,4-dioxygenase alpha chain
分子量 formula_weight	22278.8 kDa
EC 编号 ec_number	1.13.11.3
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,E,G,I,K
原子数 atom_count	21546

PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF

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	Protocatechuate 3,4-dioxygenase beta chain
分子量 formula_weight	26747.4 kDa
EC 编号 ec_number	1.13.11.3
突变 mutation	Y408H
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,D,F,H,J,L

PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRHRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC

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	3,4-DIHYDROXYBENZOIC ACID
分子量 formula_weight	154.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 4 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	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	786

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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	d1ykpa_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.3 — Prealbumin-like
超家族 Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
家族 Family family	b.3.6.1 — Aromatic compound dioxygenase

结构域编号 domain_id	d1ykpb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.3 — Prealbumin-like
超家族 Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
家族 Family family	b.3.6.1 — Aromatic compound dioxygenase

结构域编号 domain_id	d1ykpc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.3 — Prealbumin-like
超家族 Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
家族 Family family	b.3.6.1 — Aromatic compound dioxygenase

结构域编号 domain_id	d1ykpd_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.3 — Prealbumin-like
超家族 Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
家族 Family family	b.3.6.1 — Aromatic compound dioxygenase

结构域编号 domain_id	d1ykpe_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.3 — Prealbumin-like
超家族 Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
家族 Family family	b.3.6.1 — Aromatic compound dioxygenase

结构域编号 domain_id	d1ykpf_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.3 — Prealbumin-like
超家族 Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
家族 Family family	b.3.6.1 — Aromatic compound dioxygenase

结构域编号 domain_id	d1ykpg_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.3 — Prealbumin-like
超家族 Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
家族 Family family	b.3.6.1 — Aromatic compound dioxygenase

结构域编号 domain_id	d1ykph_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.3 — Prealbumin-like
超家族 Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
家族 Family family	b.3.6.1 — Aromatic compound dioxygenase

结构域编号 domain_id	d1ykpi_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.3 — Prealbumin-like
超家族 Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
家族 Family family	b.3.6.1 — Aromatic compound dioxygenase

结构域编号 domain_id	d1ykpj_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.3 — Prealbumin-like
超家族 Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
家族 Family family	b.3.6.1 — Aromatic compound dioxygenase

结构域编号 domain_id	d1ykpk_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.3 — Prealbumin-like
超家族 Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
家族 Family family	b.3.6.1 — Aromatic compound dioxygenase

结构域编号 domain_id	d1ykpl_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.3 — Prealbumin-like
超家族 Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
家族 Family family	b.3.6.1 — Aromatic compound dioxygenase

CATH v4.4 (12 domains)

结构域编号 domain_id	1ykpA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Aromatic compound dioxygenase

结构域编号 domain_id	1ykpB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Aromatic compound dioxygenase

结构域编号 domain_id	1ykpC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Aromatic compound dioxygenase

结构域编号 domain_id	1ykpD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Aromatic compound dioxygenase

结构域编号 domain_id	1ykpE00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Aromatic compound dioxygenase

结构域编号 domain_id	1ykpF00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Aromatic compound dioxygenase

结构域编号 domain_id	1ykpG00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Aromatic compound dioxygenase

结构域编号 domain_id	1ykpH00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Aromatic compound dioxygenase

结构域编号 domain_id	1ykpI00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Aromatic compound dioxygenase

结构域编号 domain_id	1ykpJ00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Aromatic compound dioxygenase

结构域编号 domain_id	1ykpK00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Aromatic compound dioxygenase

结构域编号 domain_id	1ykpL00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Aromatic compound dioxygenase

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7. 引用文献 (1)

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晶胞边长 a length_a	196.190 Å
晶胞边长 b length_b	127.970 Å
晶胞边长 c length_c	134.180 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	97.68 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	I 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.410 Å
最低分辨率 resolution_low	30.370 Å
R 因子 r_factor	0.1450
R_work r_work	0.1450
R_free r_free	0.2110

fit	/app/data/saxs_computation/yk/1ykp/1ykp.fit
pddf	/app/data/pr_computation/yk/1ykp/1ykp.pr.out
profile	/app/data/saxs_computation/yk/1ykp/1ykp.dat

Protocatechuate 3,4-Dioxygenase Y408H mutant bound to DHB

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

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) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)