9mnn

Crystal structure of L. monocytogenes MenD with Mg2+ and intermediate I bound

Method: X-RAY DIFFRACTION D_max: 88.0 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	9mnn
沉积日期 deposition_date	2024-12-22
结构标题 title	Crystal structure of L. monocytogenes MenD with Mg2+ and intermediate I bound
关键词 keywords	SEPHCHC synthase Decarboxylase ThDP-dependent enzyme, TRANSFERASE; TRANSFERASE
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	26.87 Å
回转半径 Rg (电子) rg_electron	25.82 Å
零角强度 I(0) i0	66298800.00
分子量 molecular_weight	64901.0 kDa
排除体积 excluded_volume	81780 Å³
包络体积 envelope_volume	96625 Å³
水化壳体积 shell_volume	31101 Å³
包络直径 envelope_diameter	92.5 Å
壳层 Rg shell_rg	33.29 Å
包络 Rg envelope_rg	26.03 Å
形状 Rg shape_rg	25.83 Å
总 Rg total_rg	26.57 Å
总原子数 total_atoms	4567
残基数 n_residues	579
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	88.0 Å
Rg (实空间) rg_real	26.82 Å
Rg 误差 (实空间) rg_real_error	0.58 Å
I(0) (实空间) i0_real	6.6300e+07
I(0) 误差 (实空间) i0_real_error	9.6410e+05
Rg (倒空间) rg_reciprocal	26.83 Å
I(0) (倒空间) i0_reciprocal	66300000.0000
解质量估计 total_estimate	0.8961
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	29.8 Å
偏度 Skewness skewness	0.272
峰度 Kurtosis kurtosis	-0.485
角度范围 angular_range	— – 0.2950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	16490000.0000
实空间数据点数 n_real_points	60
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.987

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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	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
分子量 formula_weight	64929.5 kDa
EC 编号 ec_number	2.2.1.9
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	4606

GAMVTNHEQVLTDYLAAFIEELVQAGVKEAIISPGSRSTPLALMMAEHPILKIYVDVDERSAGFFALGLAKASKRPVVLLCTSGTAAANYFPAVAEANLSQIPLIVLTADRPHELRNVGAPQAMDQLHLYGSHVKDFTDMALPENSEEMLRYAKWHGSRAVDIAMKTPRGPVHLNFPLREPLVPILEPSPFTATGKKHHHVHIYYTHEVLDDSSIQKMVTECTGKKGVFVVGPIDKKELEQPMVDLAKKLGWPILADPLSGLRSYGALDEVVIDQYDAFLKEAEILDKLTPEVVIRFGSMPVSKPLKNWLEQLSDIRFYVVDPGAAWKDPIKAVTDMIHCDERFLLDIMQQNMPDDAKDAAWLSRWTSYNKVAREIVLAEMANTTILEEGKIVAELRRLLPDKAGLFIGNSMPIRDVDTYFSQIDKKIKMLANRGANGIDGVVSSALGASVVFQPMFLLIGDLSFYHDMNGLLMAKKYKMNLTIVIVNNDGGGIFSFLPQANEPKYFESLFGTSTELDFRFAAAFYDADYHEAKSVDELEEAIDKASYHKGLDIIEVKTNRHENKANHQALWAKIADALKALN

来源 Source

来源生物 organism	Listeria monocytogenes 10403S
NCBI 分类编号 ncbi_taxonomy_id	393133
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	;(4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid ;
分子量 formula_weight	527.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	27

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7. 引用文献 (1)

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晶胞边长 a length_a	175.226 Å
晶胞边长 b length_b	175.226 Å
晶胞边长 c length_c	100.228 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	12

空间群 space_group	P 64 2 2
空间群编号 int_tables_number	181
晶系 crystal_system	hexagonal

分辨率 resolution	2.790 Å
最低分辨率 resolution_low	45.160 Å
R 因子 r_factor	0.1901
R_work r_work	0.1868
R_free r_free	0.2502

fit	/app/data/saxs_computation/mn/9mnn/9mnn.fit
pddf	/app/data/pr_computation/mn/9mnn/9mnn.pr.out
profile	/app/data/saxs_computation/mn/9mnn/9mnn.dat

Crystal structure of L. monocytogenes MenD with Mg2+ and intermediate I bound

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