9dae

Cryo-EM Structure of the Multimeric Phosphoenolpyruvate Binding Domain of Staphylothermus marinus Phosphoenolpyruvate Synthase

Method: ELECTRON MICROSCOPY D_max: 164.3 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9dae
沉积日期 deposition_date	2024-08-22
结构标题 title	Cryo-EM Structure of the Multimeric Phosphoenolpyruvate Binding Domain of Staphylothermus marinus Phosphoenolpyruvate Synthase
关键词 keywords	phosphoenolpyruvate, enzyme, multimeric, pyruvate, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
实验方法 method	ELECTRON MICROSCOPY

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	63.17 Å
回转半径 Rg (电子) rg_electron	62.06 Å
零角强度 I(0) i0	9663680000.00
分子量 molecular_weight	883420.0 kDa
排除体积 excluded_volume	1125800 Å³
包络体积 envelope_volume	1561900 Å³
水化壳体积 shell_volume	196810 Å³
包络直径 envelope_diameter	176.6 Å
壳层 Rg shell_rg	75.50 Å
包络 Rg envelope_rg	58.62 Å
形状 Rg shape_rg	62.12 Å
总 Rg total_rg	62.04 Å
总原子数 total_atoms	62232
残基数 n_residues	7752
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	164.3 Å
Rg (实空间) rg_real	62.43 Å
Rg 误差 (实空间) rg_real_error	0.55 Å
I(0) (实空间) i0_real	9.6640e+09
I(0) 误差 (实空间) i0_real_error	1.6050e+08
Rg (倒空间) rg_reciprocal	63.79 Å
I(0) (倒空间) i0_reciprocal	9686000000.0000
解质量估计 total_estimate	0.8423
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	92.0 Å
偏度 Skewness skewness	-0.155
峰度 Kurtosis kurtosis	-0.615
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	21850000000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.983; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (2)

Entity 1 polymer

描述 description	Phosphoenolpyruvate synthase
分子量 formula_weight	95153.9 kDa
EC 编号 ec_number	2.7.9.2
来源方法 src_method	man
拷贝数 entity_count	24

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,E,G,I,K,M,O,Q,S,V,X,Z,BA,DA,FA,HA,JA,LA,NA,PA,RA,TA,VA
原子数 atom_count	62232

MGSSHHHHHHSSGSNVPKEKRFIVWLDEVTKDDVVLVGGKNANLGEMIRAGIPVPPGFAVTAYAYKYFIEKTGLKDKIYPLLNSIDVNDKKVLDETTAKIRQWIMDTPMPPEVEEEIRKYYRELAKKIGMEPEKLRVAVRSSATAEDMPEASFAGQQDTYLNVYGEDNVVYYVKRCWASLFTSRAVFYRVAQGIPHEKSLMSVTVQKMVNSRTAGVMFTLHPVTGDEKVVVIEASWGLGESVVGGKVTPDEWVVDKQTLQIVDQKIHHKTLAIVFDPKKGKNVEIRWDENKQAWVSEEGPVDIEMVKHFHPDKPALKEEEVKRLAELALLIEKHYGRHMDIEWAVDYDIPFPDNVFIVQARLETVWSVRKEKEKAEKKAEIKGKNIVKLSEAKVLVRGLPASPGIGAGVAKVIFDPHSKEAQEFKEGEVLVTKMTDPDWVPLMKKAVAIVTDEGGMTSHAAIVSRELGIPAIVGTGNATQVIKSGIEVTVDGSRGVVYEGIVEDLVKPKEEVKAEVAGVGISPEQLLPLYPVTATKIYMNLGEPDAIEKYKDLPFDGIGLMRIEFIITDWVQYHPLYLIEQGKESLFIDKLAEGIAKVAQAIYPRPVVVRFSDFKTNEYRGLKGGEKYEPEERNPMIGWRGVSRYIHPKYEPAFRLEVRAIKKVREEMGLTNVWVMFPFVRTTWELERALKIMEEEGLKRGKDFKVWAMAEVPSIVLLADKFAEYVDGFSIGSNDLTQLILGADRDSNILAEMGYFDERDPAVLAGIKMIIEKAHSKGATVSICGQAPSVYPEIVEFLVEAGIDSISVNPDAVIATRRLVASIERKIMLKRLNKIMDKLNKLELGF

来源 Source

来源生物 organism	Staphylothermus marinus F1
NCBI 分类编号 ncbi_taxonomy_id	399550
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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	24

▶

7. 引用文献 (1)

▶

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	—

分辨率 resolution	2.24 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	1138254

fit	/app/data/saxs_computation/da/9dae/9dae.fit
pddf	/app/data/pr_computation/da/9dae/9dae.pr.out
profile	/app/data/saxs_computation/da/9dae/9dae.dat

Cryo-EM Structure of the Multimeric Phosphoenolpyruvate Binding Domain of Staphylothermus marinus Phosphoenolpyruvate Synthase

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 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)