SAXSdb — 1vrs

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1vrs
沉积日期 deposition_date	2005-06-17
结构标题 title	;Crystal structure of the disulfide-linked complex between the N-terminal and C-terminal domain of the electron transfer catalyst DsbD ;
关键词 keywords	DsbD, immunoglobulin-like, thioredoxin-like, disulfide-linked, OXIDOREDUCTASE; OXIDOREDUCTASE
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	35.40 Å
回转半径 Rg (电子) rg_electron	34.70 Å
零角强度 I(0) i0	99770600.00
分子量 molecular_weight	80109.0 kDa
排除体积 excluded_volume	100370 Å³
包络体积 envelope_volume	141930 Å³
水化壳体积 shell_volume	35518 Å³
包络直径 envelope_diameter	117.5 Å
壳层 Rg shell_rg	39.73 Å
包络 Rg envelope_rg	33.58 Å
形状 Rg shape_rg	34.68 Å
总 Rg total_rg	35.18 Å
总原子数 total_atoms	5670
残基数 n_residues	713
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	115.0 Å
Rg (实空间) rg_real	35.35 Å
Rg 误差 (实空间) rg_real_error	0.73 Å
I(0) (实空间) i0_real	9.9770e+07
I(0) 误差 (实空间) i0_real_error	1.5260e+06
Rg (倒空间) rg_reciprocal	35.38 Å
I(0) (倒空间) i0_reciprocal	99770000.0000
解质量估计 total_estimate	0.8970
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	0
主峰位置 r_peak_primary	— Å
偏度 Skewness skewness	0.193
峰度 Kurtosis kurtosis	-0.525
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	9340000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.927

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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 (3)

Entity 1 polymer

描述 description	Thiol:disulfide interchange protein dsbD
分子量 formula_weight	15982.6 kDa
EC 编号 ec_number	1.8.1.8
突变 mutation	C103S
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	5954

GLFDAPGRSQFVPADQAFAFDFQQNQHDLNLTWQIKDGYYLYRKQIRITPEHAKIADVQLPQGVWHEDEFYGKSEIYRDRLTLPVTINQASAGATLTVTYQGSADAGFCYPPETKTVPLSEVVANNAAPQPVSVPQQEQPTAQ

来源 Source

来源生物 organism	Escherichia coli str. K12 substr.
NCBI 分类编号 ncbi_taxonomy_id	316407
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Thiol:disulfide interchange protein dsbD
分子量 formula_weight	15081.9 kDa
EC 编号 ec_number	1.8.1.8
突变 mutation	C464S
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

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

ATHTAQTQTHLNFTQIKTVDELNQALVEAKGKPVMLDLYADWCVASKEFEKYTFSDPQVQKALADTVLLQANVTANDAQDVALLKHLNVLGLPTILFFDGQGQEHPQARVTGFMDAETFSAHLRDRQPHHHHHH

来源 Source

来源生物 organism	Escherichia coli str. K12 substr.
NCBI 分类编号 ncbi_taxonomy_id	316407
宿主生物 host_organism	Escherichia coli

Entity 3 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	284

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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	d1vrsa_
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.1.17 — Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)
家族 Family family	b.1.17.1 — Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)

结构域编号 domain_id	d1vrsb_
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.1.17 — Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)
家族 Family family	b.1.17.1 — Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)

结构域编号 domain_id	d1vrsc_
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.1.17 — Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)
家族 Family family	b.1.17.1 — Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)

结构域编号 domain_id	d1vrsd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.1 — Thioltransferase

结构域编号 domain_id	d1vrse_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.1 — Thioltransferase

结构域编号 domain_id	d1vrsf_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.1 — Thioltransferase

CATH v4.4 (6 domains)

结构域编号 domain_id	1vrsA00
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	1250 — Thiol:disulfide interchange protein DsbD, N-terminal domain

结构域编号 domain_id	1vrsB00
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	1250 — Thiol:disulfide interchange protein DsbD, N-terminal domain

结构域编号 domain_id	1vrsC00
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	1250 — Thiol:disulfide interchange protein DsbD, N-terminal domain

结构域编号 domain_id	1vrsD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	1vrsE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	1vrsF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

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7. 引用文献 (1)

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晶胞边长 a length_a	188.460 Å
晶胞边长 b length_b	52.600 Å
晶胞边长 c length_c	107.920 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	12

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	2.850 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.2240
R_free r_free	0.2840

fit	/app/data/saxs_computation/vr/1vrs/1vrs.fit
pddf	/app/data/pr_computation/vr/1vrs/1vrs.pr.out
profile	/app/data/saxs_computation/vr/1vrs/1vrs.dat

;Crystal structure of the disulfide-linked complex between the N-terminal and C-terminal domain of the electron transfer catalyst DsbD ;

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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 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 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)