SAXSdb — 1gm9

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1gm9
沉积日期 deposition_date	2001-09-12
结构标题 title	Crystal structures of penicillin acylase enzyme-substrate complexes: Structural insights into the catalytic mechanism
关键词 keywords	ANTIBIOTIC RESISTANCE, 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	27.58 Å
回转半径 Rg (电子) rg_electron	26.47 Å
零角强度 I(0) i0	121410000.00
分子量 molecular_weight	87009.0 kDa
排除体积 excluded_volume	108640 Å³
包络体积 envelope_volume	125160 Å³
水化壳体积 shell_volume	37753 Å³
包络直径 envelope_diameter	92.4 Å
壳层 Rg shell_rg	35.33 Å
包络 Rg envelope_rg	26.78 Å
形状 Rg shape_rg	26.44 Å
总 Rg total_rg	27.37 Å
总原子数 total_atoms	6147
残基数 n_residues	763
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	85.5 Å
Rg (实空间) rg_real	27.42 Å
Rg 误差 (实空间) rg_real_error	0.46 Å
I(0) (实空间) i0_real	1.2140e+08
I(0) 误差 (实空间) i0_real_error	1.7280e+06
Rg (倒空间) rg_reciprocal	27.47 Å
I(0) (倒空间) i0_reciprocal	121400000.0000
解质量估计 total_estimate	0.9043
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	35.4 Å
偏度 Skewness skewness	0.169
峰度 Kurtosis kurtosis	-0.484
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	35320000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.972

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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 (6)

Entity 1 polymer

描述 description	PENICILLIN G ACYLASE ALPHA SUBUNIT
分子量 formula_weight	23854.8 kDa
EC 编号 ec_number	3.5.1.11
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	6882

EQSSSEIKIVRDEYGMPHIYANDTWHLFYGYGYVVAQDRLFQMEMARRSTQGTVAEVLGKDFVKFDKDIRRNYWPDAIRAQIAALSPEDMSILQGYADGMNAWIDKVNTNPETLLPKQFNTFGFTPKRWEPFDVAMIFVGTMANRFSDSTSEIDNLALLTALKDKYGVSQGMAVFNQLKWLVNPSAPTTIAVQESNYPLKFNQQNSQTA

来源 Source

来源生物 organism	ESCHERICHIA COLI
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 polymer

描述 description	PENICILLIN G ACYLASE BETA SUBUNIT
分子量 formula_weight	62429.5 kDa
EC 编号 ec_number	3.5.1.11
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

SNMWVIGKSKAQDAKAIMVNGPQFGWYAPAYTYGIGLHGAGYDVTGNTPFAYPGLVFGHNGVISWGSTAGFGDDVDIFAERLSAEKPGYYLHNGKWVKMLSREETITVKNGQAETFTVWRTVHGNILQTDQTTQTAYAKSRAWDGKEVASLLAWTHQMKAKNWQEWTQQAAKQALTINWYYADVNGNIGYVHTGAYPDRQSGHDPRLPVPGTGKWDWKGLLPFEMNPKVYNPQSGYIANWNNSPQKDYPASDLFAFLWGGADRVTEIDRLLEQKPRLTADQAWDVIRQTSRQDLNLRLFLPTLQAATSGLTQSDPRRQLVETLTRWDGINLLNDDGKTWQQPGSAILNVWLTSMLKRTVVAAVPMPFDKWYSASGYETTQDGPTGSLNISVGAKILYEAVQGDKSPIPQAVDLFAGKPQQEVVLAALEDTWETLSKRYGNNVSNWKTPAMALTFRANNFFGVPQAAAEETRHQAEYQNRGTENDMIVFSPTTSDRPVLAWDVVAPGQSGFIAPDGTVDKHYEDQLKMYENFGRKSLWLTKQDVEAHKESQEVLHVQR

来源 Source

来源生物 organism	ESCHERICHIA COLI
NCBI 分类编号 ncbi_taxonomy_id	562
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	11

Entity 4 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	N-[(2S,4S,6R)-2-(DIHYDROXYMETHYL)-4-HYDROXY-3,3-DIMETHYL-7-OXO-4LAMBDA~4~-THIA-1-AZABICYCLO[3.2.0]HEPT-6-YL]-2-PHENYLAC ETAMIDE
分子量 formula_weight	352.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 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	701

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1gm9.1
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

CATH v4.4 (5 domains)

结构域编号 domain_id	1gm9A01
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	1gm9A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	150 —

结构域编号 domain_id	1gm9B01
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	1gm9B02
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	1gm9B03
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

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7. 引用文献 (3)

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晶胞边长 a length_a	51.200 Å
晶胞边长 b length_b	131.700 Å
晶胞边长 c length_c	64.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	105.90 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	2

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	1.800 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.1530
R_free r_free	0.1900

fit	/app/data/saxs_computation/gm/1gm9/1gm9.fit
pddf	/app/data/pr_computation/gm/1gm9/1gm9.pr.out
profile	/app/data/saxs_computation/gm/1gm9/1gm9.dat

Crystal structures of penicillin acylase enzyme-substrate complexes: Structural insights into the catalytic mechanism

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 (6)

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 non-polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (1 domains)

CATH v4.4 (5 domains)

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)