1n13

The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii

Method: X-RAY DIFFRACTION D_max: 112.2 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	1n13
沉积日期 deposition_date	2002-10-16
结构标题 title	The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii
关键词 keywords	pyruvoyl group, pyruvate, arginine decarboxylase, agmatine, arginine, LYASE; LYASE
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	34.03 Å
回转半径 Rg (电子) rg_electron	33.51 Å
零角强度 I(0) i0	151872000.00
分子量 molecular_weight	104000.0 kDa
排除体积 excluded_volume	132500 Å³
包络体积 envelope_volume	160220 Å³
水化壳体积 shell_volume	40719 Å³
包络直径 envelope_diameter	117.3 Å
壳层 Rg shell_rg	39.34 Å
包络 Rg envelope_rg	33.37 Å
形状 Rg shape_rg	33.49 Å
总 Rg total_rg	34.04 Å
总原子数 total_atoms	7292
残基数 n_residues	949
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	112.2 Å
Rg (实空间) rg_real	34.17 Å
Rg 误差 (实空间) rg_real_error	0.84 Å
I(0) (实空间) i0_real	1.5190e+08
I(0) 误差 (实空间) i0_real_error	2.7100e+06
Rg (倒空间) rg_reciprocal	34.09 Å
I(0) (倒空间) i0_reciprocal	151900000.0000
解质量估计 total_estimate	0.8484
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	35.8 Å
偏度 Skewness skewness	0.457
峰度 Kurtosis kurtosis	-0.438
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	16370000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.773; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.930; Smooth: 0.777

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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	Pyruvoyl-dependent arginine decarboxylase beta chain
分子量 formula_weight	5428.1 kDa
EC 编号 ec_number	4.1.1.19
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	8260

MNAEINPLHAYFKLPNTVSLVAGSSEGETPLNAFDGALLNAGIGNVNLIRIS

来源 Source

来源生物 organism	Methanocaldococcus jannaschii
NCBI 分类编号 ncbi_taxonomy_id	2190
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Pyruvoyl-dependent arginine decarboxylase alpha chain
分子量 formula_weight	12297.4 kDa
EC 编号 ec_number	4.1.1.19
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

XIMPPEAEIVPLPKLPMGALVPTAYGYIISDVPGETISAAISVAIPKDKSLCGLIMEYEGKCSKKEAEKTVREMAKIGFEMRGWELDRIESIAVEHTVEKLGCAFAAAALWYK

来源 Source

来源生物 organism	Methanocaldococcus jannaschii
NCBI 分类编号 ncbi_taxonomy_id	2190
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	AGMATINE
分子量 formula_weight	130.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 4 non-polymer

描述 description	(4R)-2-METHYLPENTANE-2,4-DIOL
分子量 formula_weight	118.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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	736

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1n13.1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.155 — Pyruvoyl-dependent histidine and arginine decarboxylases
超家族 Superfamily superfamily	d.155.1 — Pyruvoyl-dependent histidine and arginine decarboxylases
家族 Family family	d.155.1.2 — Arginine decarboxylase

结构域编号 domain_id	d1n13.2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.155 — Pyruvoyl-dependent histidine and arginine decarboxylases
超家族 Superfamily superfamily	d.155.1 — Pyruvoyl-dependent histidine and arginine decarboxylases
家族 Family family	d.155.1.2 — Arginine decarboxylase

结构域编号 domain_id	d1n13.3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.155 — Pyruvoyl-dependent histidine and arginine decarboxylases
超家族 Superfamily superfamily	d.155.1 — Pyruvoyl-dependent histidine and arginine decarboxylases
家族 Family family	d.155.1.2 — Arginine decarboxylase

结构域编号 domain_id	d1n13.4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.155 — Pyruvoyl-dependent histidine and arginine decarboxylases
超家族 Superfamily superfamily	d.155.1 — Pyruvoyl-dependent histidine and arginine decarboxylases
家族 Family family	d.155.1.2 — Arginine decarboxylase

结构域编号 domain_id	d1n13.5
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.155 — Pyruvoyl-dependent histidine and arginine decarboxylases
超家族 Superfamily superfamily	d.155.1 — Pyruvoyl-dependent histidine and arginine decarboxylases
家族 Family family	d.155.1.2 — Arginine decarboxylase

结构域编号 domain_id	d1n13.6
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.155 — Pyruvoyl-dependent histidine and arginine decarboxylases
超家族 Superfamily superfamily	d.155.1 — Pyruvoyl-dependent histidine and arginine decarboxylases
家族 Family family	d.155.1.2 — Arginine decarboxylase

CATH v4.4 (12 domains)

结构域编号 domain_id	1n13A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1n13B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	20 — Pyruvoyl-Dependent Histidine Decarboxylase; Chain B
同源超家族 H-superfamily homologous superfamily	10 — Pyruvoyl-Dependent Histidine Decarboxylase, subunit B

结构域编号 domain_id	1n13C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1n13D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	20 — Pyruvoyl-Dependent Histidine Decarboxylase; Chain B
同源超家族 H-superfamily homologous superfamily	10 — Pyruvoyl-Dependent Histidine Decarboxylase, subunit B

结构域编号 domain_id	1n13E00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1n13F00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	20 — Pyruvoyl-Dependent Histidine Decarboxylase; Chain B
同源超家族 H-superfamily homologous superfamily	10 — Pyruvoyl-Dependent Histidine Decarboxylase, subunit B

结构域编号 domain_id	1n13G00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1n13H00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	20 — Pyruvoyl-Dependent Histidine Decarboxylase; Chain B
同源超家族 H-superfamily homologous superfamily	10 — Pyruvoyl-Dependent Histidine Decarboxylase, subunit B

结构域编号 domain_id	1n13I00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1n13J00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	20 — Pyruvoyl-Dependent Histidine Decarboxylase; Chain B
同源超家族 H-superfamily homologous superfamily	10 — Pyruvoyl-Dependent Histidine Decarboxylase, subunit B

结构域编号 domain_id	1n13K00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1n13L00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	20 — Pyruvoyl-Dependent Histidine Decarboxylase; Chain B
同源超家族 H-superfamily homologous superfamily	10 — Pyruvoyl-Dependent Histidine Decarboxylase, subunit B

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7. 引用文献 (2)

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晶胞边长 a length_a	56.460 Å
晶胞边长 b length_b	92.880 Å
晶胞边长 c length_c	87.110 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.74 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

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	1.400 Å
最低分辨率 resolution_low	29.160 Å
R 因子 r_factor	0.1915
R_work r_work	0.1915
R_free r_free	0.2150

fit	/app/data/saxs_computation/n1/1n13/1n13.fit
pddf	/app/data/pr_computation/n1/1n13/1n13.pr.out
profile	/app/data/saxs_computation/n1/1n13/1n13.dat

The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii

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) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)