SAXSdb — 1or0

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1or0
沉积日期 deposition_date	2003-03-11
结构标题 title	Crystal Structures of Glutaryl 7-Aminocephalosporanic Acid Acylase: Insight into Autoproteolytic Activation
关键词 keywords	;Glutaryl 7-aminocephalosporanic acid, N-terminal nucleophile (Ntn) hydrolases, Glutaryl 7-aminocephalosporanic acid Acylase, HYDROLASE ;; HYDROLASE
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	43.85 Å
回转半径 Rg (电子) rg_electron	44.00 Å
零角强度 I(0) i0	354471000.00
分子量 molecular_weight	151070.0 kDa
排除体积 excluded_volume	186590 Å³
包络体积 envelope_volume	243750 Å³
水化壳体积 shell_volume	47133 Å³
包络直径 envelope_diameter	144.5 Å
壳层 Rg shell_rg	47.46 Å
包络 Rg envelope_rg	43.03 Å
形状 Rg shape_rg	43.97 Å
总 Rg total_rg	44.23 Å
总原子数 total_atoms	10617
残基数 n_residues	1323
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	139.4 Å
Rg (实空间) rg_real	44.10 Å
Rg 误差 (实空间) rg_real_error	1.24 Å
I(0) (实空间) i0_real	3.5450e+08
I(0) 误差 (实空间) i0_real_error	6.8710e+06
Rg (倒空间) rg_reciprocal	43.86 Å
I(0) (倒空间) i0_reciprocal	354400000.0000
解质量估计 total_estimate	0.8117
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	34.8 Å
偏度 Skewness skewness	0.320
峰度 Kurtosis kurtosis	-0.883
角度范围 angular_range	— – 0.1800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	30160000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.764; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.802; Smooth: 0.455

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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	Glutaryl 7-Aminocephalosporanic Acid Acylase
分子量 formula_weight	17644.2 kDa
EC 编号 ec_number	3.5.1.-
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,C
原子数 atom_count	12046

EPTSTPQAPIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPDVRQVLPVSGADVVAHAHRLMNFLYVASPGRTLGEG

来源 Source

来源生物 organism	Pseudomonas sp. SY-77-1
NCBI 分类编号 ncbi_taxonomy_id	269086
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	glutaryl acylase
分子量 formula_weight	59624.6 kDa
EC 编号 ec_number	3.5.1.-
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	B,D

SNSWAVAPGKTANGNALLLQNPHLSWTTDYFTYYEAHLVTPDFEIYGATQIGLPVIRFAFNQRMGITNTVNGMVGATNYRLTLQDGGYLYDGQVRPFERPQASYRLRQADGTTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGMLEQYFDMITADSFDDYEAALARMQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGLVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYTPKDFPSYLAPQTPHSLRAQQSVRLMSENDDLTLERFMALQLSHRAVMADRTLPDLIPAALIDPDPEVQAAARLLAAWDREFTSDSRAALLFEEWARLFAGQNFAGQAGFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRMILNDVNVPGAAGYGNLGSFRVFTWSDPDENGVRTPVHGETWVAMIEFSTPVRAYGLMSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNFKPHHHHHH

来源 Source

来源生物 organism	Pseudomonas sp. SY-77-1
NCBI 分类编号 ncbi_taxonomy_id	269086
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	1429

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1or0.1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.2 — Penicillin acylase, catalytic domain

结构域编号 domain_id	d1or0.2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.2 — Penicillin acylase, catalytic domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1or0A00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	439 — Penicillin Amidohydrolase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Penicillin Amidohydrolase, domain 1

结构域编号 domain_id	1or0B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1or0B02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1400 — Penicillin amidase (Acylase) alpha subunit, N-terminal domain
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, alpha-helical knob region

结构域编号 domain_id	1or0B03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	120 — Penicillin G acylase, beta-roll domain
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region

结构域编号 domain_id	1or0C00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	439 — Penicillin Amidohydrolase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Penicillin Amidohydrolase, domain 1

结构域编号 domain_id	1or0D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1or0D02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1400 — Penicillin amidase (Acylase) alpha subunit, N-terminal domain
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, alpha-helical knob region

结构域编号 domain_id	1or0D03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	120 — Penicillin G acylase, beta-roll domain
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region

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7. 引用文献 (1)

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晶胞边长 a length_a	229.667 Å
晶胞边长 b length_b	69.907 Å
晶胞边长 c length_c	113.726 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	97.63 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	19.950 Å
R 因子 r_factor	0.1890
R_work r_work	0.1710
R_free r_free	0.1840

fit	/app/data/saxs_computation/or/1or0/1or0.fit
pddf	/app/data/pr_computation/or/1or0/1or0.pr.out
profile	/app/data/saxs_computation/or/1or0/1or0.dat

Crystal Structures of Glutaryl 7-Aminocephalosporanic Acid Acylase: Insight into Autoproteolytic Activation

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) 10 domains

SCOP 2.08 (2 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)