SAXSdb — 1jma

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1jma
沉积日期 deposition_date	2001-07-17
结构标题 title	CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS GLYCOPROTEIN D BOUND TO THE CELLULAR RECEPTOR HVEA/HVEM
关键词 keywords	V-type Ig molecule and TNFR superfamily, Viral protein; VIRAL 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	24.88 Å
回转半径 Rg (电子) rg_electron	24.08 Å
零角强度 I(0) i0	29773100.00
分子量 molecular_weight	40420.0 kDa
排除体积 excluded_volume	49954 Å³
包络体积 envelope_volume	63690 Å³
水化壳体积 shell_volume	23247 Å³
包络直径 envelope_diameter	96.9 Å
壳层 Rg shell_rg	29.47 Å
包络 Rg envelope_rg	24.87 Å
形状 Rg shape_rg	24.00 Å
总 Rg total_rg	24.93 Å
总原子数 total_atoms	2818
残基数 n_residues	359
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	93.6 Å
Rg (实空间) rg_real	25.05 Å
Rg 误差 (实空间) rg_real_error	0.94 Å
I(0) (实空间) i0_real	2.9770e+07
I(0) 误差 (实空间) i0_real_error	4.5250e+05
Rg (倒空间) rg_reciprocal	25.01 Å
I(0) (倒空间) i0_reciprocal	29770000.0000
解质量估计 total_estimate	0.6600
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	26.7 Å
偏度 Skewness skewness	0.548
峰度 Kurtosis kurtosis	0.066
角度范围 angular_range	— – 0.3200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4350000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.636; Stabil: 1.000; Sysdev: 0.338; Positv: 1.000; Valcen: 0.662; Smooth: 0.992

▶

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

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	HERPESVIRUS ENTRY MEDIATOR
分子量 formula_weight	17768.0 kDa
突变 mutation	ECTODOMAIN OF THE FULL PROTEIN
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B
原子数 atom_count	2885

LPSCKEDEYPVGSECCPKCSPGYRVKEACGELTGTVCEPCPPGTYIAHLNGLSKCLQCQMCDPAMGLRASRNCSRTENAVCGCSPGHFCIVQDGDHCAACRAYATSSPGQRVQKGGTESQDTLCQNCPPGTFSPNGTLEECQHQTKCSWLVTKAGAGTSSSHHHHHH

来源 Source

来源生物 organism	Human herpesvirus 1
通用名 common_name	Herpes simplex virus type 1
NCBI 分类编号 ncbi_taxonomy_id	10298
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 polymer

描述 description	GLYCOPROTEIN D
分子量 formula_weight	32315.7 kDa
突变 mutation	C-TERMINAL TRUNCATION AT RESIDUE 285
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

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

KYALADASLKMADPNRFRGKDLPVLDQLTDPPGVRRVYHIQAGLPDPFQPPSLPITVYYAVLERACRSVLLNAPSEAPQIVRGASEDVRKQPYNLTIAWFRMGGNCAIPITVMEYTECSYNKSLGACPIRTQPRWNYYDSFSAVSEDNLGFLMHAPAFETAGTYLRLVKINDWTEITQFILEHRAKGSCKYALPLRIPPSACLSPQAYQQGVTVDSIGMLPRFIPENQRTVAVYSLKIAGWHGPKAPYTSTLLPPELSETPNATQPELAPEDPEDSALLEDPVGTHHHHH

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	Spodoptera frugiperda

Entity 3 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

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	5

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	49

▼

6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1jmaa_
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.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d1jmab1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.24 — TNF receptor-like
超家族 Superfamily superfamily	g.24.1 — TNF receptor-like
家族 Family family	g.24.1.1 — TNF receptor-like

结构域编号 domain_id	d1jmab2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.24 — TNF receptor-like
超家族 Superfamily superfamily	g.24.1 — TNF receptor-like
家族 Family family	g.24.1.1 — TNF receptor-like

CATH v4.4 (3 domains)

结构域编号 domain_id	1jmaA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	230 — Glycoprotein D; Chain: A;
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1jmaB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

结构域编号 domain_id	1jmaB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

▶

7. 引用文献 (2)

▶

晶胞边长 a length_a	129.154 Å
晶胞边长 b length_b	129.154 Å
晶胞边长 c length_c	80.940 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	6

空间群 space_group	P 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	—

分辨率 resolution	2.650 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2370
R_work r_work	0.2360
R_free r_free	0.2590

fit	/app/data/saxs_computation/jm/1jma/1jma.fit
pddf	/app/data/pr_computation/jm/1jma/1jma.pr.out
profile	/app/data/saxs_computation/jm/1jma/1jma.dat

CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS GLYCOPROTEIN D BOUND TO THE CELLULAR RECEPTOR HVEA/HVEM

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

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 branched

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)