SAXSdb — 1hsa

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hsa
沉积日期 deposition_date	1992-08-11
结构标题 title	;THE THREE-DIMENSIONAL STRUCTURE OF HLA-B27 AT 2.1 ANGSTROMS RESOLUTION SUGGESTS A GENERAL MECHANISM FOR TIGHT PEPTIDE BINDING TO MHC ;
关键词 keywords	HISTOCOMPATIBILITY ANTIGEN; HISTOCOMPATIBILITY ANTIGEN
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	32.21 Å
回转半径 Rg (电子) rg_electron	31.43 Å
零角强度 I(0) i0	135902000.00
分子量 molecular_weight	88690.0 kDa
排除体积 excluded_volume	109230 Å³
包络体积 envelope_volume	143210 Å³
水化壳体积 shell_volume	38403 Å³
包络直径 envelope_diameter	100.7 Å
壳层 Rg shell_rg	38.19 Å
包络 Rg envelope_rg	30.92 Å
形状 Rg shape_rg	31.41 Å
总 Rg total_rg	32.03 Å
总原子数 total_atoms	6266
残基数 n_residues	768
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	103.5 Å
Rg (实空间) rg_real	32.20 Å
Rg 误差 (实空间) rg_real_error	0.67 Å
I(0) (实空间) i0_real	1.3590e+08
I(0) 误差 (实空间) i0_real_error	1.8430e+06
Rg (倒空间) rg_reciprocal	32.21 Å
I(0) (倒空间) i0_reciprocal	135900000.0000
解质量估计 total_estimate	0.6931
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	101.4 Å
偏度 Skewness skewness	0.287
峰度 Kurtosis kurtosis	-0.587
角度范围 angular_range	— – 0.2450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	18570000.0000
实空间数据点数 n_real_points	50
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 0.096; Positv: 1.000; Valcen: 0.992; Smooth: 0.953

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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	CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-B*2705)
分子量 formula_weight	31928.2 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	6706

GSHSMRYFHTSVSRPGRGEPRFITVGYVDDTLFVRFDSDAASPREEPRAPWIEQEGPEYWDRETQICKAKAQTDREDLRTLLRYYNQSEAGSHTLQNMYGCDVGPDGRLLRGYHQDAYDGKDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGECVEWLRRYLENGKETLQRADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

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

Entity 2 polymer

描述 description	BETA 2-MICROGLOBULIN
分子量 formula_weight	11748.2 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

IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

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

Entity 3 polymer

描述 description	MODEL PEPTIDE SEQUENCE - ARAAAAAAA
分子量 formula_weight	743.8 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	C,F

ARAAAAAAA

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	440

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1hsaa1
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	d1hsaa2
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	d1hsab_
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	d1hsad1
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	d1hsad2
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	d1hsae_
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)

CATH v4.4 (6 domains)

结构域编号 domain_id	1hsaA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — MHC class I-like antigen recognition-like

结构域编号 domain_id	1hsaA02
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	1hsaB00
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	1hsaD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — MHC class I-like antigen recognition-like

结构域编号 domain_id	1hsaD02
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	1hsaE00
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 (9)

The three-dimensional structure of HLA-B27 at 2.1 A resolution suggests a general mechanism for tight peptide binding to MHC.

Cell(Cambridge,Mass.) (1992)

PMID: 1525820 · DOI: 10.1016/0092-8674(92)90252-8 PRIMARY

Crystallization and Preliminary X-Ray Diffraction Studies of the Human Major Histocompatibility Antigen Hla-B27

Proteins (1992)

The Structure of Hla-B27 Reveals Nonamer Self-Peptides Bound in an Extended Conformation

Nature (1991)

Identification of Self Peptides Bound to Purified Hla-B27

Nature (1991)

Refined Structure of the Human Histocompatibility Antigen Hla-A2 at 2.6 Angstroms Resolution

J.Mol.Biol. (1991)

Specificity Pockets for the Side Chains of Peptide Antigens in Hla-Aw68

Nature (1989)

Structure of the Human Class I Histocompatibility Antigen, Hla-A2

Nature (1987)

The Foreign Antigen Binding Site and T Cell Recognition Regions of Class I Histocompatibility Antigens

Nature (1987)

Crystallization and X-Ray Diffraction Studies on the Histocompatibility Antigens Hla-A2 and Hla-A28 from Human Cell Membranes

J.Mol.Biol. (1985)

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晶胞边长 a length_a	45.100 Å
晶胞边长 b length_b	69.800 Å
晶胞边长 c length_c	81.100 Å
晶胞夹角 α angle_alpha	80.30 °
晶胞夹角 β angle_beta	88.60 °
晶胞夹角 γ angle_gamma	89.90 °
晶胞分子数 Z z_pdb	2

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

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	0.2030
R_work r_work	0.2030
R_free r_free	—

fit	/app/data/saxs_computation/hs/1hsa/1hsa.fit
pddf	/app/data/pr_computation/hs/1hsa/1hsa.pr.out
profile	/app/data/saxs_computation/hs/1hsa/1hsa.dat

;THE THREE-DIMENSIONAL STRUCTURE OF HLA-B27 AT 2.1 ANGSTROMS RESOLUTION SUGGESTS A GENERAL MECHANISM FOR TIGHT PEPTIDE BINDING TO MHC ;

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

5. 实体与聚合体信息 (4)

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 water

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. 引用文献 (9)

8. 文件与曲线 (10)

Files (7)

Curves (3)