SAXSdb — 1m1z

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1m1z
沉积日期 deposition_date	2002-06-20
结构标题 title	BETA-LACTAM SYNTHETASE APO ENZYME
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

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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	31.82 Å
回转半径 Rg (电子) rg_electron	30.65 Å
零角强度 I(0) i0	174334000.00
分子量 molecular_weight	103260.0 kDa
排除体积 excluded_volume	128620 Å³
包络体积 envelope_volume	160800 Å³
水化壳体积 shell_volume	42426 Å³
包络直径 envelope_diameter	98.5 Å
壳层 Rg shell_rg	38.96 Å
包络 Rg envelope_rg	30.58 Å
形状 Rg shape_rg	30.65 Å
总 Rg total_rg	31.32 Å
总原子数 total_atoms	7280
残基数 n_residues	970
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	101.1 Å
Rg (实空间) rg_real	31.71 Å
Rg 误差 (实空间) rg_real_error	0.92 Å
I(0) (实空间) i0_real	1.7430e+08
I(0) 误差 (实空间) i0_real_error	2.9160e+06
Rg (倒空间) rg_reciprocal	31.76 Å
I(0) (倒空间) i0_reciprocal	174300000.0000
解质量估计 total_estimate	0.9062
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	36.4 Å
偏度 Skewness skewness	0.216
峰度 Kurtosis kurtosis	-0.560
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	52710000.0000
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: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.979

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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 (2)

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	7883

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 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	603

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1m1za1
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	d1m1za2
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	d1m1zb1
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	d1m1zb2
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	1m1zA01
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	1m1zA02
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	1m1zB01
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	1m1zB02
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

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7. 引用文献 (1)

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晶胞边长 a length_a	61.179 Å
晶胞边长 b length_b	97.469 Å
晶胞边长 c length_c	80.968 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.42 °
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	1.950 Å
最低分辨率 resolution_low	23.880 Å
R 因子 r_factor	—
R_work r_work	0.1970
R_free r_free	0.2310

fit	/app/data/saxs_computation/m1/1m1z/1m1z.fit
pddf	/app/data/pr_computation/m1/1m1z/1m1z.pr.out
profile	/app/data/saxs_computation/m1/1m1z/1m1z.dat

BETA-LACTAM SYNTHETASE APO ENZYME

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