8itt

Crystal structure of lysophosphatidylcholine in complex with human serum albumin and myristate

Method: X-RAY DIFFRACTION D_max: 168.4 Å Quality: REASONABLE

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	8itt
沉积日期 deposition_date	2023-03-22
结构标题 title	Crystal structure of lysophosphatidylcholine in complex with human serum albumin and myristate
关键词 keywords	lysophosphatidylcholine, myristate, human serum albumin, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	53.80 Å
回转半径 Rg (电子) rg_electron	54.17 Å
零角强度 I(0) i0	244392000.00
分子量 molecular_weight	131020.0 kDa
排除体积 excluded_volume	164270 Å³
包络体积 envelope_volume	252300 Å³
水化壳体积 shell_volume	40096 Å³
包络直径 envelope_diameter	180.1 Å
壳层 Rg shell_rg	54.53 Å
包络 Rg envelope_rg	52.34 Å
形状 Rg shape_rg	54.18 Å
总 Rg total_rg	54.15 Å
总原子数 total_atoms	9167
残基数 n_residues	1158
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	168.4 Å
Rg (实空间) rg_real	54.33 Å
Rg 误差 (实空间) rg_real_error	1.93 Å
I(0) (实空间) i0_real	2.4440e+08
I(0) 误差 (实空间) i0_real_error	5.1450e+06
Rg (倒空间) rg_reciprocal	53.31 Å
I(0) (倒空间) i0_reciprocal	244000000.0000
解质量估计 total_estimate	0.6869
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	34.9 Å
偏度 Skewness skewness	0.379
峰度 Kurtosis kurtosis	-0.921
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	13040000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.472; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.520; Smooth: 0.003

▶

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

▶

5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	Albumin
分子量 formula_weight	66102.7 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	9167

HKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEPERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTLSEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLVAASEAA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Komagataella pastoris

Entity 2 non-polymer

描述 description	MYRISTIC ACID
分子量 formula_weight	228.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 3 non-polymer

描述 description	[1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE
分子量 formula_weight	468.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	95.262 Å
晶胞边长 b length_b	38.467 Å
晶胞边长 c length_c	182.455 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	104.78 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	3.030 Å
最低分辨率 resolution_low	47.630 Å
R 因子 r_factor	0.2610
R_work r_work	0.2610
R_free r_free	0.2910

fit	/app/data/saxs_computation/it/8itt/8itt.fit
pddf	/app/data/pr_computation/it/8itt/8itt.pr.out
profile	/app/data/saxs_computation/it/8itt/8itt.dat

Crystal structure of lysophosphatidylcholine in complex with human serum albumin and myristate

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