SAXSdb — 1w27

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1w27
沉积日期 deposition_date	2004-06-29
结构标题 title	Phenylalanine ammonia-lyase (PAL) from Petroselinum crispum
关键词 keywords	LYASE, PHENYLPROPANOID METABOLISM, MIO; 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	38.67 Å
回转半径 Rg (电子) rg_electron	38.65 Å
零角强度 I(0) i0	344416000.00
分子量 molecular_weight	150870.0 kDa
排除体积 excluded_volume	189070 Å³
包络体积 envelope_volume	237390 Å³
水化壳体积 shell_volume	52825 Å³
包络直径 envelope_diameter	171.1 Å
壳层 Rg shell_rg	42.50 Å
包络 Rg envelope_rg	39.94 Å
形状 Rg shape_rg	38.65 Å
总 Rg total_rg	38.88 Å
总原子数 total_atoms	10592
残基数 n_residues	1378
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	158.0 Å
Rg (实空间) rg_real	39.15 Å
Rg 误差 (实空间) rg_real_error	2.62 Å
I(0) (实空间) i0_real	3.4440e+08
I(0) 误差 (实空间) i0_real_error	7.8730e+06
Rg (倒空间) rg_reciprocal	38.84 Å
I(0) (倒空间) i0_reciprocal	344300000.0000
解质量估计 total_estimate	0.7538
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	38.5 Å
偏度 Skewness skewness	0.724
峰度 Kurtosis kurtosis	0.507
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	111900000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.407; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.609; Smooth: 0.967

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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	PHENYLALANINE AMMONIA-LYASE 1
分子量 formula_weight	77878.7 kDa
EC 编号 ec_number	4.3.1.5
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	11663

MENGNGATTNGHVNGNGMDFCMKTEDPLYWGIAAEAMTGSHLDEVKKMVAEYRKPVVKLGGETLTISQVAAISARDGSGVTVELSEAARAGVKASSDWVMDSMNKGTDSYGVTTGFGATSHRRTKQGGALQKELIRFLNAGIFGNGSDNTLPHSATRAAMLVRINTLLQGYSGIRFEILEAITKFLNQNITPCLPLRGTITASGDLVPLSYIAGLLTGRPNSKAVGPTGVILSPEEAFKLAGVEGGFFELQPKEGLALVNGTAVGSGMASMVLFEANILAVLAEVMSAIFAEVMQGKPEFTDHLTHKLKHHPGQIEAAAIMEHILDGSAYVKAAQKLHEMDPLQKPKQDRYALRTSPQWLGPQIEVIRSSTKMIEREINSVNDNPLIDVSRNKAIHGGNFQGTPIGVSMDNTRLAIAAIGKLMFAQFSELVNDFYNNGLPSNLSGGRNPSLDYGFKGAEIAMASYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISSRKTSEAVEILKLMSTTFLVGLCQAIDLRHLEENLKSTVKNTVSSVAKRVLTMGVNGELHPSRFCEKDLLRVVDREYIFAYIDDPCSATYPLMQKLRQTLVEHALKNGDNERNLSTSIFQKIATFEDELKALLPKEVESARAALESGNPAIPNRIEECRSYPLYKFVRKELGTEYLTGEKVTSPGEEFEKVFIAMSKGEIIDPLLECLESWNGAPLPIC

来源 Source

来源生物 organism	PETROSELINUM CRISPUM
通用名 common_name	PARSLEY
NCBI 分类编号 ncbi_taxonomy_id	4043
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	2,3-DIHYDROXY-1,4-DITHIOBUTANE
分子量 formula_weight	154.3 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	1071

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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	d1w27a_
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	d1w27b_
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 (6 domains)

结构域编号 domain_id	1w27A01
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	1w27A02
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	1w27A03
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	1w27B01
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	1w27B02
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	1w27B03
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	119.960 Å
晶胞边长 b length_b	160.810 Å
晶胞边长 c length_c	141.330 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	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	1.700 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.1680
R_work r_work	0.1660
R_free r_free	0.1990

fit	/app/data/saxs_computation/w2/1w27/1w27.fit
pddf	/app/data/pr_computation/w2/1w27/1w27.pr.out
profile	/app/data/saxs_computation/w2/1w27/1w27.dat

Phenylalanine ammonia-lyase (PAL) from Petroselinum crispum

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