SAXSdb — 1lsh

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1lsh
沉积日期 deposition_date	2002-05-17
结构标题 title	LIPID-PROTEIN INTERACTIONS IN LIPOVITELLIN
关键词 keywords	;LIPOVITELLIN, VITELLOGENIN, LIPOPROTEIN, PLASMA APOLIPOPROTE APOLIPOPROTEIN B, APOB, MICROSOMAL TRIGLYCERIDE TRANSFER PR BOUNDARY LIPID, PHOSPHOLIPID STRUCTURE, LIPID BINDING PROTEIN ;; LIPID BINDING PROTEIN
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	36.07 Å
回转半径 Rg (电子) rg_electron	34.69 Å
零角强度 I(0) i0	234155000.00
分子量 molecular_weight	134340.0 kDa
排除体积 excluded_volume	173610 Å³
包络体积 envelope_volume	227460 Å³
水化壳体积 shell_volume	54070 Å³
包络直径 envelope_diameter	120.1 Å
壳层 Rg shell_rg	41.77 Å
包络 Rg envelope_rg	34.40 Å
形状 Rg shape_rg	34.74 Å
总 Rg total_rg	35.09 Å
总原子数 total_atoms	9426
残基数 n_residues	1128
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	118.1 Å
Rg (实空间) rg_real	35.94 Å
Rg 误差 (实空间) rg_real_error	0.85 Å
I(0) (实空间) i0_real	2.3420e+08
I(0) 误差 (实空间) i0_real_error	4.3260e+06
Rg (倒空间) rg_reciprocal	36.03 Å
I(0) (倒空间) i0_reciprocal	234200000.0000
解质量估计 total_estimate	0.8064
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	51.0 Å
偏度 Skewness skewness	0.196
峰度 Kurtosis kurtosis	-0.302
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	35890000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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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 (5)

Entity 1 polymer

描述 description	LIPOVITELLIN (LV-1N, LV-1C)
分子量 formula_weight	117469.5 kDa
来源方法 src_method	nat
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	10935

QFQPGKVYRYSYDAFSISGLPEPGVNRAGLSGEMKIEIHGHTHNQATLKITQVNLKYFLGPWPSDSFYPLTGGYDHFIQQLEVPVRFDYSAGRIGDIYAPPQVTDTAVNIVRGILNLFQLSLKKNQQTFELQETGVEGICQTTYVVQEGYRTNEMAVVKTKDLNNCDHKVYKTMGTAYAERCPTCQKMNKNLRSTAVYNYAIFDEPSGYIIKSAHSEEIQQLSVFDIKEGNVVIESRQKLILEGIQSAPAASQAASLQNRGGLMYKFPSSAITKMSSLFVTKGKNLESEIHTVLKHLVENNQLSVHEDAPAKFLRLTAFLRNVDAGVLQSIWHKLHQQKDYRRWILDAVPAMATSEALLFLKRTLASEQLTSAEATQIVASTLSNQQATRESLSYARELLNTSFIRNRPILRKTAVLGYGSLVFRYCANTVSCPDELLQPLHDLLSQSSDRAKEEEIVLALKALGNAGQPNSIKKIQRFLPGQGKSLDEYSTRVQAEAIMALRNIAKRDPRKVQEIVLPIFLNVAIKSELRIRSCIVFFESKPSVALVSMVAVRLRREPNLQVASFVYSQMRSLSRSSNPEFRDVAAACSVAIKMLGSKLDRLGCRYSKAVHVDTFNARTMAGVSADYFRINSPSGPLPRAVAAKIRGQGMGYASDIVEFGLRAEGLQELLYRGSQEQDAYGTALDRQTLLRSGQARSHVSSIHDTLRKLSDWKSVPEERPLASGYVKVHGQEVVFAELDKKMMQRISQLWHSARSHHAAAQEQIGAVVSKLEQGMDVLLTKGYVVSEVRYMQPVCIGIPMDLNLLVSGVTTNRANLSASFSSLPADMKLADLLATNIELRVAATTSMSQHAVAIMGLTTDLAKAGMQTHYKTSAGLGVNGKIEMNARESNFKASLKPFQQKTVVVLSTMESIVFVRDPSGSRILPVLPPKMTLDKGLISQQQQQPHHQQQPHQHGQDQARAAYQRPWASHEFSPAEQKQIHDIMTARPVMRRKQSCSKSAALSSKVCFSARLRNAAFIRNALLYKITGDYVSKVYVQPTSSKAQITKVELELQAG

Entity 2 polymer

描述 description	LIPOVITELLIN (LV-2)
分子量 formula_weight	35110.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

KYVPQRKPQTSRRHTPASSSSSSSSSSSSSSSSSSSDSDMTVSAESFEKHSKPKVVIVLRAVRADGKQQGLQTTLYYGLTSNGLPKAKIVAVELSDLSVWKLCAKFRLSAHMKAKAAIGWGKNCQQYRAMLEASTGNLQSHPAARVDIKWGRLPSSLQRAKNALLENGAPVIASKLEMEIMPKANQKHQVSVILAAMTPRRMNIIVKLPKVTYFQQGILLPFTFPSPRFWDRPEGSQSDSLPAQIASAFSGIVQDPVASACELNEQSLTTFNGAFFNYDMPESCYHVLAQECSSRPPFIVLIKLDSERRISLELQLDDK

Entity 3 non-polymer

描述 description	di-heneicosanoyl phosphatidyl choline
分子量 formula_weight	875.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

Entity 4 non-polymer

描述 description	UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID
分子量 formula_weight	478.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	43

Entity 5 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	1122

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6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1lsha1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.118 — alpha-alpha superhelix
超家族 Superfamily superfamily	a.118.4 — Lipovitellin-phosvitin complex, superhelical domain
家族 Family family	a.118.4.1 — Lipovitellin-phosvitin complex, superhelical domain

结构域编号 domain_id	d1lsha2
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.7 — Lipovitellin-phosvitin complex; beta-sheet shell regions
超家族 Superfamily superfamily	f.7.1 — Lipovitellin-phosvitin complex; beta-sheet shell regions
家族 Family family	f.7.1.1 — Lipovitellin-phosvitin complex; beta-sheet shell regions

结构域编号 domain_id	d1lsha3
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.7 — Lipovitellin-phosvitin complex; beta-sheet shell regions
超家族 Superfamily superfamily	f.7.1 — Lipovitellin-phosvitin complex; beta-sheet shell regions
家族 Family family	f.7.1.1 — Lipovitellin-phosvitin complex; beta-sheet shell regions

结构域编号 domain_id	d1lshb_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.7 — Lipovitellin-phosvitin complex; beta-sheet shell regions
超家族 Superfamily superfamily	f.7.1 — Lipovitellin-phosvitin complex; beta-sheet shell regions
家族 Family family	f.7.1.1 — Lipovitellin-phosvitin complex; beta-sheet shell regions

CATH v4.4 (5 domains)

结构域编号 domain_id	1lshA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	230 — Lipovitellin-phosvitin complex; beta-sheet shell regions
同源超家族 H-superfamily homologous superfamily	10 — Lipovitellin; beta-sheet shell regions, chain A

结构域编号 domain_id	1lshA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	25 — Alpha Horseshoe
拓扑 Topology topology	10 — Leucine-rich Repeat Variant
同源超家族 H-superfamily homologous superfamily	20 — Vitellinogen, superhelical

结构域编号 domain_id	1lshA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	50 — Outer Surface Protein A; domain 2
同源超家族 H-superfamily homologous superfamily	20 — Lipovitellin. Chain A, domain 3

结构域编号 domain_id	1lshA04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	80 — Lipovitellin-phosvitin complex, chain A, domain 4
同源超家族 H-superfamily homologous superfamily	10 — Lipovitellin-phosvitin complex, chain A, domain 4

结构域编号 domain_id	1lshB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	90 — Lipovitellin-phosvitin complex; beta-sheet shell regions
同源超家族 H-superfamily homologous superfamily	10 — Vitellinogen, beta-sheet shell domain

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7. 引用文献 (2)

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晶胞边长 a length_a	190.170 Å
晶胞边长 b length_b	84.520 Å
晶胞边长 c length_c	89.530 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	100.39 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	21.600 Å
R 因子 r_factor	0.1930
R_work r_work	0.1930
R_free r_free	0.2550

fit	/app/data/saxs_computation/ls/1lsh/1lsh.fit
pddf	/app/data/pr_computation/ls/1lsh/1lsh.pr.out
profile	/app/data/saxs_computation/ls/1lsh/1lsh.dat

LIPID-PROTEIN INTERACTIONS IN LIPOVITELLIN

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 (5)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (4 domains)

CATH v4.4 (5 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)