1fv1

;STRUCTURAL BASIS FOR THE BINDING OF AN IMMUNODOMINANT PEPTIDE FROM MYELIN BASIC PROTEIN IN DIFFERENT REGISTERS BY TWO HLA-DR2 ALLELES ;

Method: X-RAY DIFFRACTION D_max: 99.9 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	1fv1
沉积日期 deposition_date	2000-09-18
结构标题 title	;STRUCTURAL BASIS FOR THE BINDING OF AN IMMUNODOMINANT PEPTIDE FROM MYELIN BASIC PROTEIN IN DIFFERENT REGISTERS BY TWO HLA-DR2 ALLELES ;
关键词 keywords	MHC class II DR2a, IMMUNE SYSTEM; IMMUNE SYSTEM
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	30.83 Å
回转半径 Rg (电子) rg_electron	30.23 Å
零角强度 I(0) i0	127236000.00
分子量 molecular_weight	88691.0 kDa
排除体积 excluded_volume	110430 Å³
包络体积 envelope_volume	144770 Å³
水化壳体积 shell_volume	40120 Å³
包络直径 envelope_diameter	105.3 Å
壳层 Rg shell_rg	37.37 Å
包络 Rg envelope_rg	30.17 Å
形状 Rg shape_rg	30.20 Å
总 Rg total_rg	30.96 Å
总原子数 total_atoms	6275
残基数 n_residues	775
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	99.9 Å
Rg (实空间) rg_real	30.80 Å
Rg 误差 (实空间) rg_real_error	0.75 Å
I(0) (实空间) i0_real	1.2720e+08
I(0) 误差 (实空间) i0_real_error	2.2180e+06
Rg (倒空间) rg_reciprocal	30.81 Å
I(0) (倒空间) i0_reciprocal	127200000.0000
解质量估计 total_estimate	0.8846
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	37.2 Å
偏度 Skewness skewness	0.346
峰度 Kurtosis kurtosis	-0.225
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	14730000.0000
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: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.835

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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 (6)

Entity 1 polymer

描述 description	MAJOR HISTOCOMPATIBILITY COMPLEX ALPHA CHAIN
分子量 formula_weight	21084.8 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,D
原子数 atom_count	6795

IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD

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	Escherichia coli

Entity 2 polymer

描述 description	MAJOR HISTOCOMPATIBILITY COMPLEX BETA CHAIN
分子量 formula_weight	22231.6 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	B,E

GDTRPRFLQQDKYECHFFNGTERVRFLHRDIYNQEEDLRFDSDVGEYRAVTELGRPDAEYWNSQKDFLEDRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPARTQTLQHHNLLVCSVNGFYPGSIEVRWFRNSQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA

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	Escherichia coli

Entity 3 polymer

描述 description	MYELIN BASIC PROTEIN
分子量 formula_weight	2278.6 kDa
来源方法 src_method	syn
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

NPVVHFFKNIVTPRTPPPSQ

Entity 4 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	3

Entity 5 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 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	494

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1fv1a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1fv1a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.19 — MHC antigen-recognition domain
超家族 Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
家族 Family family	d.19.1.1 — MHC antigen-recognition domain

结构域编号 domain_id	d1fv1b1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1fv1b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.19 — MHC antigen-recognition domain
超家族 Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
家族 Family family	d.19.1.1 — MHC antigen-recognition domain

结构域编号 domain_id	d1fv1d1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1fv1d2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.19 — MHC antigen-recognition domain
超家族 Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
家族 Family family	d.19.1.1 — MHC antigen-recognition domain

结构域编号 domain_id	d1fv1e1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1fv1e2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.19 — MHC antigen-recognition domain
超家族 Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
家族 Family family	d.19.1.1 — MHC antigen-recognition domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1fv1A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

结构域编号 domain_id	1fv1A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1fv1B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

结构域编号 domain_id	1fv1B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1fv1D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

结构域编号 domain_id	1fv1D02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1fv1E01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

结构域编号 domain_id	1fv1E02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

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7. 引用文献 (1)

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晶胞边长 a length_a	63.189 Å
晶胞边长 b length_b	114.892 Å
晶胞边长 c length_c	63.175 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.90 °
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	1.900 Å
最低分辨率 resolution_low	100.000 Å
R 因子 r_factor	0.2330
R_work r_work	0.2330
R_free r_free	0.2670

fit	/app/data/saxs_computation/fv/1fv1/1fv1.fit
pddf	/app/data/pr_computation/fv/1fv1/1fv1.pr.out
profile	/app/data/saxs_computation/fv/1fv1/1fv1.dat

;STRUCTURAL BASIS FOR THE BINDING OF AN IMMUNODOMINANT PEPTIDE FROM MYELIN BASIC PROTEIN IN DIFFERENT REGISTERS BY TWO HLA-DR2 ALLELES ;

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 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)