8e72

Treponema lecithinolyticum beta-glucuronidase in complex with a ciprofloxacin-glucuronide conjugate

Method: X-RAY DIFFRACTION D_max: 97.5 Å Quality: EXCELLENT

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8e72
沉积日期 deposition_date	2022-08-23
结构标题 title	Treponema lecithinolyticum beta-glucuronidase in complex with a ciprofloxacin-glucuronide conjugate
关键词 keywords	Glycoside hydrolase family 2, TIM barrel domain, 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	31.80 Å
回转半径 Rg (电子) rg_electron	30.76 Å
零角强度 I(0) i0	279901000.00
分子量 molecular_weight	134910.0 kDa
排除体积 excluded_volume	168680 Å³
包络体积 envelope_volume	199120 Å³
水化壳体积 shell_volume	51235 Å³
包络直径 envelope_diameter	99.3 Å
壳层 Rg shell_rg	39.91 Å
包络 Rg envelope_rg	30.83 Å
形状 Rg shape_rg	30.75 Å
总 Rg total_rg	31.49 Å
总原子数 total_atoms	9516
残基数 n_residues	1194
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	97.5 Å
Rg (实空间) rg_real	31.61 Å
Rg 误差 (实空间) rg_real_error	0.45 Å
I(0) (实空间) i0_real	2.7990e+08
I(0) 误差 (实空间) i0_real_error	3.7790e+06
Rg (倒空间) rg_reciprocal	31.69 Å
I(0) (倒空间) i0_reciprocal	279900000.0000
解质量估计 total_estimate	0.9033
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	39.0 Å
偏度 Skewness skewness	0.164
峰度 Kurtosis kurtosis	-0.517
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	92220000.0000
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: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.937

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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	Glycosyl hydrolase family 2, TIM barrel domain protein
分子量 formula_weight	72102.3 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	10245

HHHHHHSSGVDLGTENLYFQSNAMLYPILTQSRMLIDLSGTWRFKLDDGSGFEKKWYEKTLDDAQLMPVPSSYNDIKESADLRDHYGWVFYQRDLNIPAYLKTQRIVLRFAAVTHSAKVYVNGTLLCEHKGGFLPFETEIPENLIRDENLLTVAVDNRIDHSTLPVGREDESNVLGGSFFPYTPTKKQNKPNFDFFNYCGITRPVKLYTTPKDAYISDITLTSSLENNTARINYKIDTKGSAHTAIGVYTKQGVCVAQTENTGTEGSLTIENAVLWEPLKPYLYEVKISFGEDRYTLPYGIRSVAVKGNKFLINNKPFYFKGYGKHEDTFPAGRGLNMPMNAKDISLMKWQGANSFRTSHYPYSEEMMRLCDEEGIVVIDETTAVGVHLNFGGGAALKDGKRVNTFDPIEQGGIRTQSHHKEVIKDLIARDKNHACVVMWSIANEADTGSKGAYEYFKPLFDLARELDPQKRPCTLVSLQMVNYKEDCTIKLSDVFCLNRYYGWYTCGADLQAAEKMCREELEFWNSLGKPFMYTEYGADTVMGLHDTTDSMFTEEYQVEYYKTNHKVTDTLDCFIGEQVWNFADFATSQGLIRVQGNKKGLFTRDRKPKLAAHYFKERWSKIPDFGYKK

来源 Source

来源生物 organism	Treponema lecithinolyticum
NCBI 分类编号 ncbi_taxonomy_id	53418
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	3-carboxy-1-cyclopropyl-6-fluoro-7-(4-beta-D-glucopyranuronosyl-3,4-dihydropyrazin-1(2H)-yl)-4-oxo-1,4-dihydroquinoline
分子量 formula_weight	505.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	633

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6. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

结构域编号 domain_id	8e72A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	80 — Glycosidases

结构域编号 domain_id	8e72B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	80 — Glycosidases

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7. 引用文献 (1)

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晶胞边长 a length_a	94.406 Å
晶胞边长 b length_b	94.406 Å
晶胞边长 c length_c	288.014 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	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	P 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	1.950 Å
最低分辨率 resolution_low	66.760 Å
R 因子 r_factor	0.1849
R_work r_work	0.1843
R_free r_free	0.2124

fit	/app/data/saxs_computation/e7/8e72/8e72.fit
pddf	/app/data/pr_computation/e7/8e72/8e72.pr.out
profile	/app/data/saxs_computation/e7/8e72/8e72.dat