SAXSdb — 1mb9

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1mb9
沉积日期 deposition_date	2002-08-02
结构标题 title	BETA-LACTAM SYNTHETASE COMPLEXED WITH ATP
关键词 keywords	CLAVULANIC ACID, ASPARAGINE SYNTHETASE, BETA-LACTAM SYNTHETASE, CARBOXYETHYL ARGININE, DEOXYGUANIDINOPROCLAVAMINIC ACID, HYDROLASE; HYDROLASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	31.83 Å
回转半径 Rg (电子) rg_electron	30.69 Å
零角强度 I(0) i0	187699000.00
分子量 molecular_weight	105960.0 kDa
排除体积 excluded_volume	131440 Å³
包络体积 envelope_volume	163510 Å³
水化壳体积 shell_volume	42895 Å³
包络直径 envelope_diameter	99.2 Å
壳层 Rg shell_rg	39.09 Å
包络 Rg envelope_rg	30.65 Å
形状 Rg shape_rg	30.70 Å
总 Rg total_rg	31.35 Å
总原子数 total_atoms	7458
残基数 n_residues	982
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	99.2 Å
Rg (实空间) rg_real	31.72 Å
Rg 误差 (实空间) rg_real_error	0.77 Å
I(0) (实空间) i0_real	1.8770e+08
I(0) 误差 (实空间) i0_real_error	3.0710e+06
Rg (倒空间) rg_reciprocal	31.77 Å
I(0) (倒空间) i0_reciprocal	187700000.0000
解质量估计 total_estimate	0.9059
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	37.7 Å
偏度 Skewness skewness	0.204
峰度 Kurtosis kurtosis	-0.573
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	67150000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.952; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.921

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (6)

Entity 1 polymer

描述 description	BETA-LACTAM SYNTHETASE
分子量 formula_weight	54601.6 kDa
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	7960

MGAPVLPAAFGFLASARTGGGRAPGPVFATRGSHTDIDTPQGERSLAATLVHAPSVAPDRAVARSLTGAPTTAVLAGEIYNRDELLSVLPAGPAPEGDAELVLRLLERYDLHAFRLVNGRFATVVRTGDRVLLATDHAGSVPLYTCVAPGEVRASTEAKALAAHRDPKGFPLADARRVAGLTGVYQVPAGAVMDIDLGSGTAVTHRTWTPGLSRRILPEGEAVAAVRAALEKAVAQRVTPGDTPLVVLSGGIDSSGVAACAHRAAGELDTVSMGTDTSNEFREARAVVDHLRTRHREITIPTTELLAQLPYAVWASESVDPDIIEYLLPLTALYRALDGPERRILTGYGADIPLGGMHREDRLPALDTVLAHDMATFDGLNEMSPVLSTLAGHWTTHPYWDREVLDLLVSLEAGLKRRHGRDKWVLRAAMADALPAETVNRPKLGVHEGSGTTSSFSRLLLDHGVAEDRVHEAKRQVVRELFDLTVGGGRHPSEVDTDDVVRSVADRTARGAA

来源 Source

来源生物 organism	Streptomyces clavuligerus
NCBI 分类编号 ncbi_taxonomy_id	1901
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	PYROPHOSPHATE 2-
分子量 formula_weight	176.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	ADENOSINE MONOPHOSPHATE
分子量 formula_weight	347.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	470

▼

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1mb9a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
家族 Family family	c.26.2.1 — N-type ATP pyrophosphatases

结构域编号 domain_id	d1mb9a2
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.153.1.1 — Class II glutamine amidotransferases

结构域编号 domain_id	d1mb9b1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
家族 Family family	c.26.2.1 — N-type ATP pyrophosphatases

结构域编号 domain_id	d1mb9b2
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.153.1.1 — Class II glutamine amidotransferases

CATH v4.4 (4 domains)

结构域编号 domain_id	1mb9A01
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	1mb9A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	620 — HUPs

结构域编号 domain_id	1mb9B01
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	1mb9B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	620 — HUPs

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	61.252 Å
晶胞边长 b length_b	97.571 Å
晶胞边长 c length_c	81.313 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.69 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	2.110 Å
最低分辨率 resolution_low	24.780 Å
R 因子 r_factor	—
R_work r_work	0.2100
R_free r_free	0.2510

fit	/app/data/saxs_computation/mb/1mb9/1mb9.fit
pddf	/app/data/pr_computation/mb/1mb9/1mb9.pr.out
profile	/app/data/saxs_computation/mb/1mb9/1mb9.dat

BETA-LACTAM SYNTHETASE COMPLEXED WITH ATP

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution