8yr5

Crystal structure of E. coli phosphatidylserine synthase in apo state

Method: X-RAY DIFFRACTION D_max: 252.6 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	8yr5
沉积日期 deposition_date	2024-03-20
结构标题 title	Crystal structure of E. coli phosphatidylserine synthase in apo state
关键词 keywords	Apo, Phospholipid metabolism, Peripheral membrane protein, Phosphatidylserine, MEMBRANE PROTEIN, 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	66.41 Å
回转半径 Rg (电子) rg_electron	66.55 Å
零角强度 I(0) i0	5364440000.00
分子量 molecular_weight	622360.0 kDa
排除体积 excluded_volume	781220 Å³
包络体积 envelope_volume	1157500 Å³
水化壳体积 shell_volume	147530 Å³
包络直径 envelope_diameter	221.1 Å
壳层 Rg shell_rg	65.97 Å
包络 Rg envelope_rg	64.22 Å
形状 Rg shape_rg	66.57 Å
总 Rg total_rg	66.49 Å
总原子数 total_atoms	43895
残基数 n_residues	5282
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	252.6 Å
Rg (实空间) rg_real	70.94 Å
Rg 误差 (实空间) rg_real_error	1.77 Å
I(0) (实空间) i0_real	5.4180e+09
I(0) 误差 (实空间) i0_real_error	1.0810e+08
Rg (倒空间) rg_reciprocal	66.02 Å
I(0) (倒空间) i0_reciprocal	5357000000.0000
解质量估计 total_estimate	0.8413
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	73.7 Å
偏度 Skewness skewness	0.657
峰度 Kurtosis kurtosis	0.027
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	1.0260
最高正则化参数 α highest_alpha	589800000.0000
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: 0.500; Stabil: 0.855; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.906

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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	CDP-diacylglycerol--serine O-phosphatidyltransferase
分子量 formula_weight	53998.8 kDa
EC 编号 ec_number	2.7.8.8
来源方法 src_method	man
拷贝数 entity_count	12

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,K,L
原子数 atom_count	43895

MGSHHHHHHGSLSKFKRNKHQQHLAQLPKISQSVDDVDFFYAPADFRETLLEKIASAKQRICIVALYLEQDDGGKGILNALYEAKRQRPELDVRVLVDWHRAQRGRIGAAASNTNADWYCRMAQENPGVDVPVYGVPINTREALGVLHFKGFIIDDSVLYSGASLNDVYLHQHDKYRYDRYHLIRNRKMSDIMFEWVTQNIMNGRGVNRLDDVNRPKSPEIKNDIRLFRQELRDAAYHFQGDADNDQLSVTPLVGLGKSSLLNKTIFHLMPCAEQKLTICTPYFNLPAILVRNIIQLLREGKKVEIIVGDKTANDFYIPEDEPFKIIGALPYLYEINLRRFLSRLQYYVNTDQLVVRLWKDDDNTYHLKGMWVDDKWMLITGNNLNPRAWRLDLENAILIHDPQLELAPQREKELELIREHTTIVKHYRDLQSIADYPVKVRKLIRRLRRIRIDRLISRIL

来源 Source

来源生物 organism	Escherichia coli str. K-12 substr. MG1655
NCBI 分类编号 ncbi_taxonomy_id	511145
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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	24

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7. 引用文献 (1)

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晶胞边长 a length_a	94.040 Å
晶胞边长 b length_b	94.100 Å
晶胞边长 c length_c	194.750 Å
晶胞夹角 α angle_alpha	88.24 °
晶胞夹角 β angle_beta	87.70 °
晶胞夹角 γ angle_gamma	60.07 °
晶胞分子数 Z z_pdb	12

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

分辨率 resolution	2.830 Å
最低分辨率 resolution_low	48.640 Å
R 因子 r_factor	0.2439
R_work r_work	0.2419
R_free r_free	0.2848

fit	/app/data/saxs_computation/yr/8yr5/8yr5.fit
pddf	/app/data/pr_computation/yr/8yr5/8yr5.pr.out
profile	/app/data/saxs_computation/yr/8yr5/8yr5.dat

Crystal structure of E. coli phosphatidylserine synthase in apo state

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

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)