9e0q

CryoEM structure of inducible Lysine decarboxylase from Hafnia alvei D-hydrazino-Lysine analog at 2.3 Angstrom resolution

Method: ELECTRON MICROSCOPY D_max: 258.1 Å Quality: GOOD

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	9e0q
沉积日期 deposition_date	2024-10-18
最后修订 last_revision	2025-07-30
结构标题 title	CryoEM structure of inducible Lysine decarboxylase from Hafnia alvei D-hydrazino-Lysine analog at 2.3 Angstrom resolution
关键词 keywords	L-Lysine decarboxylase, cadaverine, D-alpha-hydrazone inhibitor, LYASE; LYASE
实验方法 method	ELECTRON MICROSCOPY

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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	64.68 Å
回转半径 Rg (电子) rg_electron	64.03 Å
零角强度 I(0) i0	17730500000.00
分子量 molecular_weight	748840.0 kDa
排除体积 excluded_volume	725340 Å³
包络体积 envelope_volume	1352500 Å³
水化壳体积 shell_volume	168110 Å³
包络直径 envelope_diameter	191.0 Å
壳层 Rg shell_rg	71.44 Å
包络 Rg envelope_rg	61.85 Å
形状 Rg shape_rg	63.97 Å
总 Rg total_rg	64.21 Å
总原子数 total_atoms	56580
残基数 n_residues	7100
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	258.1 Å
Rg (实空间) rg_real	69.07 Å
Rg 误差 (实空间) rg_real_error	1.89 Å
I(0) (实空间) i0_real	1.7950e+10
I(0) 误差 (实空间) i0_real_error	3.3800e+08
Rg (倒空间) rg_reciprocal	64.96 Å
I(0) (倒空间) i0_reciprocal	17750000000.0000
解质量估计 total_estimate	0.8570
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	86.0 Å
偏度 Skewness skewness	0.659
峰度 Kurtosis kurtosis	0.751
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	0.7371
最高正则化参数 α highest_alpha	767900000.0000
实空间数据点数 n_real_points	25
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.613; Stabil: 0.827; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.867

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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 (3)

Entity 1 polymer

描述 description	Lysine decarboxylase, inducible
分子量 formula_weight	80205.3 kDa
来源方法 src_method	man
拷贝数 entity_count	10

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J
原子数 atom_count	57307

MNIIAILNHMGVYFKEEPIRELHKALEALDFQIVYPNDREDLLKLIDNNARLCGVIFDWDTYNLDLCEEISAMNEHLPVYAFANTHSTLDVSLNDLRLNVEFFEYALGAAQDIAQKIRQSTDAYIDEILPPLTKALFNYVKEGKYTFCTPGHMGGTAFQKSPVGSIFYDFFGANAMKSDISISVGELGSLLDHSGPHKEAEEYIARTFNAERSYMVTNGTSTANKIVGMYSAPAGSTVLIDRNCHKSLTHLMMMSDITPIYFRPTRNAYGILGGIPKSEFQHDTIAERVAQTPNATWPVHAVVTNSTYDGLLYNTDYIKEALDVKSIHFDSAWVPYTNFSPIYKGLCGMSGGRVEGKVIYETQSTHKLLAAFSQASMIHVKGDINEETFNEAYMMHTSTSPHYGIVASTETAAAMMKGNAGKRLINGSIERAIRFRKEIKRLNSESEGWFFDVWQPEGIDEAKCWPLDSKDNWHGFKDIDNDHMYLDPIKVTLLTPGMQKDGSMADTGIPASIVSKYLDEHGIIVEKTGPYNMLFLFSIGIDKTKALSLLRALTDFKRSYDLNLRVKNMLPSLYREDPEFYENMRIQELAQGIHALIQHHNLPDLMYRAFEVLPTMVMNPHAAFQMELRGQTEEVYLEEMIGKVNANMILPYPPGVPLVMPGEMLTEESRPVLEFLQMLCEIGAHYPGFETDIHGAYRQADGRYTVKVIK

来源 Source

来源生物 organism	Hafnia alvei ATCC 51873
NCBI 分类编号 ncbi_taxonomy_id	1002364
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

描述 description	(2R)-6-amino-2-[(2E)-2-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)hydrazin-1-yl]hexanoic acid
分子量 formula_weight	390.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

Entity 3 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	727

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7. 引用文献 (2)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	triclinic

分辨率 resolution	2.30 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	360000

fit	/app/data/saxs_computation/e0/9e0q/9e0q.fit
pddf	/app/data/pr_computation/e0/9e0q/9e0q.pr.out
profile	/app/data/saxs_computation/e0/9e0q/9e0q.dat