SAXSdb — 1m2x

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1m2x
沉积日期 deposition_date	2002-06-26
结构标题 title	Crystal Structure of the metallo-beta-lactamase BlaB of Chryseobacterium meningosepticum in complex with the inhibitor D-captopril
关键词 keywords	ALPHA-BETA/BETA-ALPHA FOLD., 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	32.72 Å
回转半径 Rg (电子) rg_electron	32.51 Å
零角强度 I(0) i0	159905000.00
分子量 molecular_weight	101470.0 kDa
排除体积 excluded_volume	126860 Å³
包络体积 envelope_volume	162710 Å³
水化壳体积 shell_volume	41645 Å³
包络直径 envelope_diameter	103.6 Å
壳层 Rg shell_rg	39.51 Å
包络 Rg envelope_rg	31.97 Å
形状 Rg shape_rg	32.51 Å
总 Rg total_rg	33.04 Å
总原子数 total_atoms	7127
残基数 n_residues	874
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	104.0 Å
Rg (实空间) rg_real	32.59 Å
Rg 误差 (实空间) rg_real_error	0.71 Å
I(0) (实空间) i0_real	1.5990e+08
I(0) 误差 (实空间) i0_real_error	2.5120e+06
Rg (倒空间) rg_reciprocal	32.65 Å
I(0) (倒空间) i0_reciprocal	159900000.0000
解质量估计 total_estimate	0.9022
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	45.5 Å
偏度 Skewness skewness	0.147
峰度 Kurtosis kurtosis	-0.577
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	108200000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; 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	class B carbapenemase BlaB-1
分子量 formula_weight	25372.5 kDa
EC 编号 ec_number	3.5.2.6
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	8034

DVKIEKLKDNLYVYTTYNTFNGTKYAANAVYLVTDKGVVVIDCPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKIGAKTYSTKMTDSILAKENKPRAQYTFDNNKSFKVGKSEFQVYYPGKGHTADNVVVWFPKEKVLVGGCIIKSADSKDLGYIGEAYVNDWTQSVHNIQQKFSGAQYVVAGHDDWKDQRSIQHTLDLINEYQQKQKASN

来源 Source

来源生物 organism	Elizabethkingia meningoseptica
NCBI 分类编号 ncbi_taxonomy_id	238
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 4 non-polymer

描述 description	1-(3-MERCAPTO-2-METHYL-PROPIONYL)-PYRROLIDINE-2-CARBOXYLIC ACID
分子量 formula_weight	217.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 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	4

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	719

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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	d1m2xa_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
超家族 Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
家族 Family family	d.157.1.1 — Zn metallo-beta-lactamase

结构域编号 domain_id	d1m2xb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
超家族 Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
家族 Family family	d.157.1.1 — Zn metallo-beta-lactamase

结构域编号 domain_id	d1m2xc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
超家族 Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
家族 Family family	d.157.1.1 — Zn metallo-beta-lactamase

结构域编号 domain_id	d1m2xd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
超家族 Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
家族 Family family	d.157.1.1 — Zn metallo-beta-lactamase

CATH v4.4 (4 domains)

结构域编号 domain_id	1m2xA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	15 — Metallo-beta-lactamase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

结构域编号 domain_id	1m2xB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	15 — Metallo-beta-lactamase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

结构域编号 domain_id	1m2xC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	15 — Metallo-beta-lactamase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

结构域编号 domain_id	1m2xD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	15 — Metallo-beta-lactamase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

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7. 引用文献 (1)

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晶胞边长 a length_a	159.685 Å
晶胞边长 b length_b	159.685 Å
晶胞边长 c length_c	97.815 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	120.00 °
晶胞分子数 Z z_pdb	36

空间群 space_group	H 3
空间群编号 int_tables_number	146
晶系 crystal_system	—

分辨率 resolution	1.500 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	—
R_work r_work	0.1900
R_free r_free	0.2080

fit	/app/data/saxs_computation/m2/1m2x/1m2x.fit
pddf	/app/data/pr_computation/m2/1m2x/1m2x.pr.out
profile	/app/data/saxs_computation/m2/1m2x/1m2x.dat

Crystal Structure of the metallo-beta-lactamase BlaB of Chryseobacterium meningosepticum in complex with the inhibitor D-captopril

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution