1ykm

Protocatechuate 3,4-Dioxygenase Y408E mutant

Method: X-RAY DIFFRACTION D_max: 157.8 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	1ykm
沉积日期 deposition_date	2005-01-18
结构标题 title	Protocatechuate 3,4-Dioxygenase Y408E mutant
关键词 keywords	catechol, protocatechuate, 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	48.55 Å
回转半径 Rg (电子) rg_electron	47.76 Å
零角强度 I(0) i0	1284010000.00
分子量 molecular_weight	293000.0 kDa
排除体积 excluded_volume	363980 Å³
包络体积 envelope_volume	503260 Å³
水化壳体积 shell_volume	84659 Å³
包络直径 envelope_diameter	160.8 Å
壳层 Rg shell_rg	55.13 Å
包络 Rg envelope_rg	46.57 Å
形状 Rg shape_rg	47.77 Å
总 Rg total_rg	47.99 Å
总原子数 total_atoms	20688
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	157.8 Å
Rg (实空间) rg_real	48.39 Å
Rg 误差 (实空间) rg_real_error	1.19 Å
I(0) (实空间) i0_real	1.2840e+09
I(0) 误差 (实空间) i0_real_error	2.2160e+07
Rg (倒空间) rg_reciprocal	48.55 Å
I(0) (倒空间) i0_reciprocal	1284000000.0000
解质量估计 total_estimate	0.8998
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	59.2 Å
偏度 Skewness skewness	0.170
峰度 Kurtosis kurtosis	-0.631
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	190700000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.912

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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 (4)

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	22002

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	26738.3 kDa
EC 编号 ec_number	1.13.11.3
突变 mutation	Y408E
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

PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRERHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC

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	6

Entity 4 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	1314

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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	d1ykma_
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	d1ykmb1
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	d1ykmc_
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	d1ykmd_
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	d1ykme_
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	d1ykmf_
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	d1ykmg_
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	d1ykmh_
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	d1ykmi_
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	d1ykmj_
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	d1ykmk_
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	d1ykml_
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	1ykmA00
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	1ykmB00
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	1ykmC00
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	1ykmD00
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	1ykmE00
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	1ykmF00
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	1ykmG00
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	1ykmH00
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	1ykmI00
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	1ykmJ00
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	1ykmK00
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	1ykmL00
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	196.612 Å
晶胞边长 b length_b	127.728 Å
晶胞边长 c length_c	134.321 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	97.66 °
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	2.220 Å
最低分辨率 resolution_low	7.810 Å
R 因子 r_factor	0.1690
R_work r_work	0.1690
R_free r_free	0.1990

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

Protocatechuate 3,4-Dioxygenase Y408E mutant

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 (4)

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 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)