1t6p

Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides

Method: X-RAY DIFFRACTION D_max: 212.7 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	1t6p
沉积日期 deposition_date	2004-05-06
结构标题 title	Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides
关键词 keywords	triple helix coiled coil; MIO; cinnamate, 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	61.19 Å
回转半径 Rg (电子) rg_electron	61.37 Å
零角强度 I(0) i0	4664410000.00
分子量 molecular_weight	569750.0 kDa
排除体积 excluded_volume	709690 Å³
包络体积 envelope_volume	932270 Å³
水化壳体积 shell_volume	123830 Å³
包络直径 envelope_diameter	210.5 Å
壳层 Rg shell_rg	63.65 Å
包络 Rg envelope_rg	60.96 Å
形状 Rg shape_rg	61.41 Å
总 Rg total_rg	61.29 Å
总原子数 total_atoms	39729
残基数 n_residues	5107
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	212.7 Å
Rg (实空间) rg_real	61.41 Å
Rg 误差 (实空间) rg_real_error	2.61 Å
I(0) (实空间) i0_real	4.6640e+09
I(0) 误差 (实空间) i0_real_error	1.0550e+08
Rg (倒空间) rg_reciprocal	60.95 Å
I(0) (倒空间) i0_reciprocal	4661000000.0000
解质量估计 total_estimate	0.8408
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	57.3 Å
偏度 Skewness skewness	0.366
峰度 Kurtosis kurtosis	-0.615
角度范围 angular_range	— – 0.1300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	2657000000.0000
实空间数据点数 n_real_points	27
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.719; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.771

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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 (2)

Entity 1 polymer

描述 description	phenylalanine ammonia-lyase
分子量 formula_weight	77655.9 kDa
EC 编号 ec_number	4.3.1.5
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	40380

MAPSLDSISHSFANGVASAKQAVNGASTNLAVAGSHLPTTQVTQVDIVEKMLAAPTDSTLELDGYSLNLGDVVSAARKGRPVRVKDSDEIRSKIDKSVEFLRSQLSMSVYGVTTGFGGSADTRTEDAISLQKALLEHQLCGVLPSSFDSFRLGRGLENSLPLEVVRGAMTIRVNSLTRGHSAVRLVVLEALTNFLNHGITPIVPLRGTISXDLSPLSYIAAAISGHPDSKVHVVHEGKEKILYAREAMALFNLEPVVLGPKEGLGLVNGTAVSASMATLALHDAHMLSLLSQSLTAMTVEAMVGHAGSFHPFLHDVTRPHPTQIEVAGNIRKLLEGSRFAVHHEEEVKVKDDEGILRQDRYPLRTSPQWLGPLVSDLIHAHAVLTIEAGQSTTDNPLIDVENKTSHHGGNFQAAAVANTMEKTRLGLAQIGKLNFTQLTEMLNAGMNRGLPSCLAAEDPSLSYHCKGLDIAAAAYTSELGHLANPVTTHVQPAEMANQAVNSLALISARRTTESNDVLSLLLATHLYCVLQAIDLRAIEFEFKKQFGPAIVSLIDQHFGSAMTGSNLRDELVEKVNKTLAKRLEQTNSYDLVPRWHDAFSFAAGTVVEVLSSTSLSLAAVNAWKVAAAESAISLTRQVRETFWSAASTSSPALSYLSPRTQILYAFVREELGVKARRGDVFLGKQEVTIGSNVSKIYEAIKSGRINNVLLKMLA

来源 Source

来源生物 organism	Rhodosporidium toruloides
NCBI 分类编号 ncbi_taxonomy_id	5286
宿主生物 host_organism	Escherichia coli

Entity 2 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	651

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6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1t6pa_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.127 — L-aspartase-like
超家族 Superfamily superfamily	a.127.1 — L-aspartase-like
家族 Family family	a.127.1.2 — HAL/PAL-like

结构域编号 domain_id	d1t6pb_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.127 — L-aspartase-like
超家族 Superfamily superfamily	a.127.1 — L-aspartase-like
家族 Family family	a.127.1.2 — HAL/PAL-like

结构域编号 domain_id	d1t6pc_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.127 — L-aspartase-like
超家族 Superfamily superfamily	a.127.1 — L-aspartase-like
家族 Family family	a.127.1.2 — HAL/PAL-like

结构域编号 domain_id	d1t6pd_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.127 — L-aspartase-like
超家族 Superfamily superfamily	a.127.1 — L-aspartase-like
家族 Family family	a.127.1.2 — HAL/PAL-like

结构域编号 domain_id	d1t6pe_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.127 — L-aspartase-like
超家族 Superfamily superfamily	a.127.1 — L-aspartase-like
家族 Family family	a.127.1.2 — HAL/PAL-like

结构域编号 domain_id	d1t6pf_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.127 — L-aspartase-like
超家族 Superfamily superfamily	a.127.1 — L-aspartase-like
家族 Family family	a.127.1.2 — HAL/PAL-like

结构域编号 domain_id	d1t6pg_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.127 — L-aspartase-like
超家族 Superfamily superfamily	a.127.1 — L-aspartase-like
家族 Family family	a.127.1.2 — HAL/PAL-like

结构域编号 domain_id	d1t6ph_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.127 — L-aspartase-like
超家族 Superfamily superfamily	a.127.1 — L-aspartase-like
家族 Family family	a.127.1.2 — HAL/PAL-like

CATH v4.4 (24 domains)

结构域编号 domain_id	1t6pA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	275 — Fumarase C; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

结构域编号 domain_id	1t6pA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	200 — Fumarase C; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

结构域编号 domain_id	1t6pA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	274 — Enzyme I; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	20 — Phenylalanine ammonia-lyase 1; domain 3

结构域编号 domain_id	1t6pB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	275 — Fumarase C; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

结构域编号 domain_id	1t6pB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	200 — Fumarase C; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

结构域编号 domain_id	1t6pB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	274 — Enzyme I; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	20 — Phenylalanine ammonia-lyase 1; domain 3

结构域编号 domain_id	1t6pC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	275 — Fumarase C; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

结构域编号 domain_id	1t6pC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	200 — Fumarase C; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

结构域编号 domain_id	1t6pC03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	274 — Enzyme I; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	20 — Phenylalanine ammonia-lyase 1; domain 3

结构域编号 domain_id	1t6pD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	275 — Fumarase C; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

结构域编号 domain_id	1t6pD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	200 — Fumarase C; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

结构域编号 domain_id	1t6pD03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	274 — Enzyme I; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	20 — Phenylalanine ammonia-lyase 1; domain 3

结构域编号 domain_id	1t6pE01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	275 — Fumarase C; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

结构域编号 domain_id	1t6pE02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	200 — Fumarase C; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

结构域编号 domain_id	1t6pE03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	274 — Enzyme I; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	20 — Phenylalanine ammonia-lyase 1; domain 3

结构域编号 domain_id	1t6pF01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	275 — Fumarase C; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

结构域编号 domain_id	1t6pF02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	200 — Fumarase C; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

结构域编号 domain_id	1t6pF03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	274 — Enzyme I; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	20 — Phenylalanine ammonia-lyase 1; domain 3

结构域编号 domain_id	1t6pG01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	275 — Fumarase C; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

结构域编号 domain_id	1t6pG02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	200 — Fumarase C; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

结构域编号 domain_id	1t6pG03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	274 — Enzyme I; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	20 — Phenylalanine ammonia-lyase 1; domain 3

结构域编号 domain_id	1t6pH01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	275 — Fumarase C; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

结构域编号 domain_id	1t6pH02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	200 — Fumarase C; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

结构域编号 domain_id	1t6pH03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	274 — Enzyme I; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	20 — Phenylalanine ammonia-lyase 1; domain 3

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7. 引用文献 (1)

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晶胞边长 a length_a	105.192 Å
晶胞边长 b length_b	180.973 Å
晶胞边长 c length_c	149.215 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	96.95 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

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	2.700 Å
最低分辨率 resolution_low	25.100 Å
R 因子 r_factor	—
R_work r_work	0.1944
R_free r_free	0.2532

fit	/app/data/saxs_computation/t6/1t6p/1t6p.fit
pddf	/app/data/pr_computation/t6/1t6p/1t6p.pr.out
profile	/app/data/saxs_computation/t6/1t6p/1t6p.dat

Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides

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