9e0m

CryoEM structure of holoenzyme of inducible Lysine decarboxylase from Hafnia alvei holoenzyme at 2.19 Angstrom resolution

Method: ELECTRON MICROSCOPY D_max: 234.4 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	9e0m
沉积日期 deposition_date	2024-10-18
最后修订 last_revision	2025-06-04
结构标题 title	CryoEM structure of holoenzyme of inducible Lysine decarboxylase from Hafnia alvei holoenzyme at 2.19 Angstrom resolution
关键词 keywords	L-lysine carboxylyase, pH homeostasis, cadaverine, pyridoxal-phosphate protein, 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	64.90 Å
回转半径 Rg (电子) rg_electron	64.06 Å
零角强度 I(0) i0	8853240000.00
分子量 molecular_weight	803190.0 kDa
排除体积 excluded_volume	1005600 Å³
包络体积 envelope_volume	1362400 Å³
水化壳体积 shell_volume	169070 Å³
包络直径 envelope_diameter	192.0 Å
壳层 Rg shell_rg	71.65 Å
包络 Rg envelope_rg	61.87 Å
形状 Rg shape_rg	64.02 Å
总 Rg total_rg	64.31 Å
总原子数 total_atoms	56480
残基数 n_residues	7090
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	234.4 Å
Rg (实空间) rg_real	64.59 Å
Rg 误差 (实空间) rg_real_error	2.10 Å
I(0) (实空间) i0_real	8.8550e+09
I(0) 误差 (实空间) i0_real_error	1.8940e+08
Rg (倒空间) rg_reciprocal	65.19 Å
I(0) (倒空间) i0_reciprocal	8864000000.0000
解质量估计 total_estimate	0.8651
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	78.1 Å
偏度 Skewness skewness	0.099
峰度 Kurtosis kurtosis	-0.630
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	0.0201
最高正则化参数 α highest_alpha	796500000.0000
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: 0.750; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 1.000

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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	Lysine decarboxylase, inducible
分子量 formula_weight	80433.4 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	58893

MNIIAILNHMGVYFKEEPIRELHKALEALDFQIVYPNDREDLLKLIDNNARLCGVIFDWDTYNLDLCEEISAMNEHLPVYAFANTHSTLDVSLNDLRLNVEFFEYALGAAQDIAQKIRQSTDAYIDEILPPLTKALFNYVKEGKYTFCTPGHMGGTAFQKSPVGSIFYDFFGANAMKSDISISVGELGSLLDHSGPHKEAEEYIARTFNAERSYMVTNGTSTANKIVGMYSAPAGSTVLIDRNCHKSLTHLMMMSDITPIYFRPTRNAYGILGGIPKSEFQHDTIAERVAQTPNATWPVHAVVTNSTYDGLLYNTDYIKEALDVKSIHFDSAWVPYTNFSPIYKGLCGMSGGRVEGKVIYETQSTHKLLAAFSQASMIHVKGDINEETFNEAYMMHTSTSPHYGIVASTETAAAMMKGNAGKRLINGSIERAIRFRKEIKRLNSESEGWFFDVWQPEGIDEAKCWPLDSKDNWHGFKDIDNDHMYLDPIKVTLLTPGMQKDGSMADTGIPASIVSKYLDEHGIIVEKTGPYNMLFLFSIGIDKTKALSLLRALTDFKRSYDLNLRVKNMLPSLYREDPEFYENMRIQELAQGIHALIQHHNLPDLMYRAFEVLPTMVMNPHAAFQMELRGQTEEVYLEEMIGKVNANMILPYPPGVPLVMPGEMLTEESRPVLEFLQMLCEIGAHYPGFETDIHGAYRQDGARYTVKVIK

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 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	1921

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7. 引用文献 (1)

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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	2.20 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	500000

fit	/app/data/saxs_computation/e0/9e0m/9e0m.fit
pddf	/app/data/pr_computation/e0/9e0m/9e0m.pr.out
profile	/app/data/saxs_computation/e0/9e0m/9e0m.dat

CryoEM structure of holoenzyme of inducible Lysine decarboxylase from Hafnia alvei holoenzyme at 2.19 Angstrom resolution

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)