SAXSdb — 1gk1

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1gk1
沉积日期 deposition_date	2001-08-07
结构标题 title	;Structure-based prediction of modifications in glutarylamidase to allow single-step enzymatic production of 7-aminocephalosporanic acid from cephalosporin C ;
关键词 keywords	HYDROLASE, CEPHALOSPORIN ACYLASE, GLUTARYL ACYLASE, CEPHALOSPORIN C, CATALYTIC TRIAD, NTN-HYDROLASE, X-RAZ STRUCTURE; 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	44.16 Å
回转半径 Rg (电子) rg_electron	44.30 Å
零角强度 I(0) i0	345186000.00
分子量 molecular_weight	150570.0 kDa
排除体积 excluded_volume	187030 Å³
包络体积 envelope_volume	249250 Å³
水化壳体积 shell_volume	48027 Å³
包络直径 envelope_diameter	145.1 Å
壳层 Rg shell_rg	47.66 Å
包络 Rg envelope_rg	43.26 Å
形状 Rg shape_rg	44.28 Å
总 Rg total_rg	44.53 Å
总原子数 total_atoms	10662
残基数 n_residues	1350
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	140.4 Å
Rg (实空间) rg_real	44.41 Å
Rg 误差 (实空间) rg_real_error	1.27 Å
I(0) (实空间) i0_real	3.4520e+08
I(0) 误差 (实空间) i0_real_error	6.3670e+06
Rg (倒空间) rg_reciprocal	44.16 Å
I(0) (倒空间) i0_reciprocal	345100000.0000
解质量估计 total_estimate	0.8147
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	35.1 Å
偏度 Skewness skewness	0.326
峰度 Kurtosis kurtosis	-0.864
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	30640000.0000
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: 0.784; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.817; Smooth: 0.418

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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	CEPHALOSPORIN ACYLASE
分子量 formula_weight	16941.6 kDa
EC 编号 ec_number	3.5.1.11
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	11321

QAPIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPEVRQVLPVSGADVVAHAHRLMNFLYVASPGRTLGE

来源 Source

来源生物 organism	PSEUDOMONAS SP.
NCBI 分类编号 ncbi_taxonomy_id	306
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 polymer

描述 description	CEPHALOSPORIN ACYLASE
分子量 formula_weight	58339.9 kDa
EC 编号 ec_number	3.5.1.11
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

SNSWAVAPGKTANGNALLLQNPHLSWTTDYFTYYEAHLVTPDFEIYGATQIGLPVIRFAFNQRMGITNTVNGMVGATNYRLTLQDGGYLYDGQVRPFERRQASYRLRQADGTTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGMLEQYFDMITADSFDDYEAALARMQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGLVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYTPKDFPSYLAPQTPHSLRAQQSVRLMSENDDLTLERFMALQLSHRAVMADRTLPDLIPAALIDPDPEVQAAARLLAAWDREFTSDSRAALLFEEWARLFAGQNFAGQAGFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRMILNDVNVPGAAGYGNLGSFRVFTWSDPDENGVRTPVHGETWVAMIEFSTPVRAYGLMSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNFKP

来源 Source

来源生物 organism	PSEUDOMONAS SP.
NCBI 分类编号 ncbi_taxonomy_id	306
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 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	659

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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	d1gk1.1
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	d1gk1.2
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	1gk1A00
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	1gk1B01
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	1gk1B02
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	1gk1B03
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	1gk1C00
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	1gk1D01
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	1gk1D02
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	1gk1D03
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	230.290 Å
晶胞边长 b length_b	70.440 Å
晶胞边长 c length_c	114.800 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	97.48 °
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	2.400 Å
最低分辨率 resolution_low	14.630 Å
R 因子 r_factor	0.1800
R_work r_work	0.1800
R_free r_free	0.2190

fit	/app/data/saxs_computation/gk/1gk1/1gk1.fit
pddf	/app/data/pr_computation/gk/1gk1/1gk1.pr.out
profile	/app/data/saxs_computation/gk/1gk1/1gk1.dat

;Structure-based prediction of modifications in glutarylamidase to allow single-step enzymatic production of 7-aminocephalosporanic acid from cephalosporin C ;

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

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)