SAXSdb — 1js6

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1js6
沉积日期 deposition_date	2001-08-16
结构标题 title	Crystal Structure of DOPA decarboxylase
关键词 keywords	;DOPA decarboxylase, carbiDOPA, Parkinson's disease, Vitamin B6, 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	28.60 Å
回转半径 Rg (电子) rg_electron	27.66 Å
零角强度 I(0) i0	163790000.00
分子量 molecular_weight	103460.0 kDa
排除体积 excluded_volume	130110 Å³
包络体积 envelope_volume	148960 Å³
水化壳体积 shell_volume	42966 Å³
包络直径 envelope_diameter	103.1 Å
壳层 Rg shell_rg	36.52 Å
包络 Rg envelope_rg	27.77 Å
形状 Rg shape_rg	27.67 Å
总 Rg total_rg	28.40 Å
总原子数 total_atoms	7280
残基数 n_residues	928
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	93.6 Å
Rg (实空间) rg_real	28.47 Å
Rg 误差 (实空间) rg_real_error	0.53 Å
I(0) (实空间) i0_real	1.6380e+08
I(0) 误差 (实空间) i0_real_error	2.2050e+06
Rg (倒空间) rg_reciprocal	28.53 Å
I(0) (倒空间) i0_reciprocal	163800000.0000
解质量估计 total_estimate	0.8806
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	0.221
峰度 Kurtosis kurtosis	-0.293
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	75970000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.964

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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 (3)

Entity 1 polymer

描述 description	DOPA decarboxylase
分子量 formula_weight	54002.2 kDa
EC 编号 ec_number	4.1.1.28
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	7375

MNASDFRRRGKEMVDYMADYLEGIEGRQVYPDVQPGYLRPLIPATAPQEPDTFEDILQDVEKIIMPGVTHWHSPYFFAYFPTASSYPAMLADMLCGAIGCIGFSWAASPACTELETVMMDWLGKMLQLPEAFLAGEAGEGGGVIQGSASEATLVALLAARTKVVRRLQAASPGLTQGAVLEKLVAYASDQAHSSVERAGLIGGVKLKAIPSDGKFAMRASALQEALERDKAAGLIPFFVVATLGTTSCCSFDNLLEVGPICHEEDIWLHVDAAYAGSAFICPEFRHLLNGVEFADSFNFNPHKWLLVNFDCSAMWVKRRTDLTGAFKLDPVYLKHSHQGSGLITDYRHWQLPLGRRFRSLKMWFVFRMYGVKGLQAYIRKHVQLSHEFEAFVLQDPRFEVCAEVTLGLVCFRLKGSDGLNEALLERINSARKIHLVPCRLRGQFVLRFAICSRKVESGHVRLAWEHIRGLAAELLAAEEGKAEIKS

来源 Source

来源生物 organism	Sus scrofa
通用名 common_name	pig
NCBI 分类编号 ncbi_taxonomy_id	9823
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	PYRIDOXAL-5'-PHOSPHATE
分子量 formula_weight	247.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 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	95

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1js6a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.67 — PLP-dependent transferase-like
超家族 Superfamily superfamily	c.67.1 — PLP-dependent transferases
家族 Family family	c.67.1.6 — Pyridoxal-dependent decarboxylase

结构域编号 domain_id	d1js6b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.67 — PLP-dependent transferase-like
超家族 Superfamily superfamily	c.67.1 — PLP-dependent transferases
家族 Family family	c.67.1.6 — Pyridoxal-dependent decarboxylase

CATH v4.4 (6 domains)

结构域编号 domain_id	1js6A01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1340 — dopa decarboxylase, N-terminal domain
同源超家族 H-superfamily homologous superfamily	10 — dopa decarboxylase, N-terminal domain

结构域编号 domain_id	1js6A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	640 — Aspartate Aminotransferase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

结构域编号 domain_id	1js6A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1150 — Aspartate Aminotransferase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

结构域编号 domain_id	1js6B01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1340 — dopa decarboxylase, N-terminal domain
同源超家族 H-superfamily homologous superfamily	10 — dopa decarboxylase, N-terminal domain

结构域编号 domain_id	1js6B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	640 — Aspartate Aminotransferase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

结构域编号 domain_id	1js6B03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1150 — Aspartate Aminotransferase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

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7. 引用文献 (3)

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晶胞边长 a length_a	152.860 Å
晶胞边长 b length_b	152.860 Å
晶胞边长 c length_c	86.600 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	12

空间群 space_group	P 62
空间群编号 int_tables_number	171
晶系 crystal_system	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	19.870 Å
R 因子 r_factor	0.2060
R_work r_work	0.2060
R_free r_free	0.2580

fit	/app/data/saxs_computation/js/1js6/1js6.fit
pddf	/app/data/pr_computation/js/1js6/1js6.pr.out
profile	/app/data/saxs_computation/js/1js6/1js6.dat

Crystal Structure of DOPA decarboxylase

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