1li1

;The 1.9-A crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link ;

Method: X-RAY DIFFRACTION D_max: 94.1 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	1li1
沉积日期 deposition_date	2002-04-17
结构标题 title	;The 1.9-A crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link ;
关键词 keywords	basement membrane, collagen IV, NC1 domain, covalent cross-link, protein-protein interaction, STRUCTURAL PROTEIN; STRUCTURAL 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	30.81 Å
回转半径 Rg (电子) rg_electron	29.90 Å
零角强度 I(0) i0	376612000.00
分子量 molecular_weight	150830.0 kDa
排除体积 excluded_volume	186310 Å³
包络体积 envelope_volume	210870 Å³
水化壳体积 shell_volume	54565 Å³
包络直径 envelope_diameter	99.7 Å
壳层 Rg shell_rg	39.89 Å
包络 Rg envelope_rg	30.04 Å
形状 Rg shape_rg	29.82 Å
总 Rg total_rg	30.90 Å
总原子数 total_atoms	10550
残基数 n_residues	1357
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	94.1 Å
Rg (实空间) rg_real	30.62 Å
Rg 误差 (实空间) rg_real_error	0.48 Å
I(0) (实空间) i0_real	3.7660e+08
I(0) 误差 (实空间) i0_real_error	6.2810e+06
Rg (倒空间) rg_reciprocal	30.70 Å
I(0) (倒空间) i0_reciprocal	376600000.0000
解质量估计 total_estimate	0.8925
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	40.6 Å
偏度 Skewness skewness	0.193
峰度 Kurtosis kurtosis	-0.385
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	193600000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.926

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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	Collagen alpha 1(IV)
分子量 formula_weight	25356.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,D,E
原子数 atom_count	11664

SVDHGFLVTRHSQTIDDPQCPSGTKILYHGYSLLYVQGNERAHGQDLGTAGSCLRKFSTMPFLFCNINNVCNFASRNDYSYWLSTPEPMPMSMAPITGENIRPFISRCAVCEAPAMVMAVHSQTIQIPPCPSGWSSLWIGYSFVMHTSAGAEGSGQALASPGSCLEEFRSAPFIECHGRGTCNYYANAYSFWLATIERSEMFKKPTPSTLKAGELRTHVSRCQVCMRRT

Entity 2 polymer

描述 description	Collagen alpha 2(IV)
分子量 formula_weight	25114.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,F

SVSIGYLLVKHSQTDQEPMCPVGMNKLWSGYSLLYFEGQEKAHNQDLGLAGSCLARFSTMPFLYCNPGDVCYYASRNDKSYWLSTTAPLPMMPVAEDEIKPYISRCSVCEAPAIAIAVHSQDVSIPHCPAGWRSLWIGYSFLMHTAAGDEGGGQSLVSPGSCLEDFRATPFIECNGGRGTCHYYANKYSFWLTTIPEQSFQGSPSADTLKAGLIRTHISRCQVCMKNL

Entity 3 non-polymer

描述 description	ACETATE ION
分子量 formula_weight	59.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	9

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	1114

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1li1a1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

结构域编号 domain_id	d1li1a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

结构域编号 domain_id	d1li1b1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

结构域编号 domain_id	d1li1b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

结构域编号 domain_id	d1li1c1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

结构域编号 domain_id	d1li1c2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

结构域编号 domain_id	d1li1d1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

结构域编号 domain_id	d1li1d2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

结构域编号 domain_id	d1li1e1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

结构域编号 domain_id	d1li1e2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

结构域编号 domain_id	d1li1f1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

结构域编号 domain_id	d1li1f2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

CATH v4.4 (6 domains)

结构域编号 domain_id	1li1A00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	240 — Noncollagenous (NC1) domain of collagen IV
同源超家族 H-superfamily homologous superfamily	10 — Collagen IV, non-collagenous

结构域编号 domain_id	1li1B00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	240 — Noncollagenous (NC1) domain of collagen IV
同源超家族 H-superfamily homologous superfamily	10 — Collagen IV, non-collagenous

结构域编号 domain_id	1li1C00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	240 — Noncollagenous (NC1) domain of collagen IV
同源超家族 H-superfamily homologous superfamily	10 — Collagen IV, non-collagenous

结构域编号 domain_id	1li1D00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	240 — Noncollagenous (NC1) domain of collagen IV
同源超家族 H-superfamily homologous superfamily	10 — Collagen IV, non-collagenous

结构域编号 domain_id	1li1E00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	240 — Noncollagenous (NC1) domain of collagen IV
同源超家族 H-superfamily homologous superfamily	10 — Collagen IV, non-collagenous

结构域编号 domain_id	1li1F00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	240 — Noncollagenous (NC1) domain of collagen IV
同源超家族 H-superfamily homologous superfamily	10 — Collagen IV, non-collagenous

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7. 引用文献 (1)

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晶胞边长 a length_a	234.589 Å
晶胞边长 b length_b	234.589 Å
晶胞边长 c length_c	99.492 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	36

空间群 space_group	H 3
空间群编号 int_tables_number	146
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	19.950 Å
R 因子 r_factor	0.1820
R_work r_work	0.1820
R_free r_free	0.2020

fit	/app/data/saxs_computation/li/1li1/1li1.fit
pddf	/app/data/pr_computation/li/1li1/1li1.pr.out
profile	/app/data/saxs_computation/li/1li1/1li1.dat

;The 1.9-A crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link ;

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 (4)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)