1mvk

X-ray structure of the tetrameric mutant of the B1 domain of streptococcal protein G

Method: X-RAY DIFFRACTION D_max: 117.6 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	1mvk
沉积日期 deposition_date	2002-09-25
结构标题 title	X-ray structure of the tetrameric mutant of the B1 domain of streptococcal protein G
关键词 keywords	strand-exchanged tetramer, channel, PROTEIN BINDING; PROTEIN BINDING
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	34.59 Å
回转半径 Rg (电子) rg_electron	34.63 Å
零角强度 I(0) i0	64667000.00
分子量 molecular_weight	63688.0 kDa
排除体积 excluded_volume	79483 Å³
包络体积 envelope_volume	113910 Å³
水化壳体积 shell_volume	30182 Å³
包络直径 envelope_diameter	120.9 Å
壳层 Rg shell_rg	37.18 Å
包络 Rg envelope_rg	34.21 Å
形状 Rg shape_rg	34.63 Å
总 Rg total_rg	34.84 Å
总原子数 total_atoms	4500
残基数 n_residues	557
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	117.6 Å
Rg (实空间) rg_real	34.96 Å
Rg 误差 (实空间) rg_real_error	1.32 Å
I(0) (实空间) i0_real	6.4670e+07
I(0) 误差 (实空间) i0_real_error	1.2860e+06
Rg (倒空间) rg_reciprocal	34.74 Å
I(0) (倒空间) i0_reciprocal	64650000.0000
解质量估计 total_estimate	0.8118
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	33.2 Å
偏度 Skewness skewness	0.585
峰度 Kurtosis kurtosis	-0.277
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	9602000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.763; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.766; Smooth: 0.497

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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	Immunoglobulin G binding protein G
分子量 formula_weight	6302.9 kDa
突变 mutation	T2Q, L5V, A26F, F30V, Y33F, A34F
来源方法 src_method	man
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L
原子数 atom_count	4718

MQYKVILNGKTLKGETTTEAVDAATFEKVVKQFFNDNGVDGEWTYDDATKTFTVTE

来源 Source

来源生物 organism	;Streptococcus sp. 'group G' ;
NCBI 分类编号 ncbi_taxonomy_id	1320
宿主生物 host_organism	Escherichia coli

Entity 2 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 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	218

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1mvka_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.7 — Immunoglobulin-binding domains
家族 Family family	d.15.7.1 — Immunoglobulin-binding domains

结构域编号 domain_id	d1mvkb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.7 — Immunoglobulin-binding domains
家族 Family family	d.15.7.1 — Immunoglobulin-binding domains

结构域编号 domain_id	d1mvkc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.7 — Immunoglobulin-binding domains
家族 Family family	d.15.7.1 — Immunoglobulin-binding domains

结构域编号 domain_id	d1mvkd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.7 — Immunoglobulin-binding domains
家族 Family family	d.15.7.1 — Immunoglobulin-binding domains

结构域编号 domain_id	d1mvke_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.7 — Immunoglobulin-binding domains
家族 Family family	d.15.7.1 — Immunoglobulin-binding domains

结构域编号 domain_id	d1mvkf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.7 — Immunoglobulin-binding domains
家族 Family family	d.15.7.1 — Immunoglobulin-binding domains

结构域编号 domain_id	d1mvkg_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.7 — Immunoglobulin-binding domains
家族 Family family	d.15.7.1 — Immunoglobulin-binding domains

结构域编号 domain_id	d1mvkh_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.7 — Immunoglobulin-binding domains
家族 Family family	d.15.7.1 — Immunoglobulin-binding domains

结构域编号 domain_id	d1mvki_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.7 — Immunoglobulin-binding domains
家族 Family family	d.15.7.1 — Immunoglobulin-binding domains

结构域编号 domain_id	d1mvkj_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.7 — Immunoglobulin-binding domains
家族 Family family	d.15.7.1 — Immunoglobulin-binding domains

结构域编号 domain_id	d1mvkk_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.7 — Immunoglobulin-binding domains
家族 Family family	d.15.7.1 — Immunoglobulin-binding domains

结构域编号 domain_id	d1mvkl_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.7 — Immunoglobulin-binding domains
家族 Family family	d.15.7.1 — Immunoglobulin-binding domains

CATH v4.4 (12 domains)

结构域编号 domain_id	1mvkA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1mvkB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1mvkC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1mvkD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1mvkE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1mvkF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1mvkG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1mvkH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1mvkI00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1mvkJ00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1mvkK00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1mvkL00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (3)

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晶胞边长 a length_a	76.100 Å
晶胞边长 b length_b	210.400 Å
晶胞边长 c length_c	55.300 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	90.00 °
晶胞分子数 Z z_pdb	48

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2370
R_work r_work	0.2370
R_free r_free	0.2830

fit	/app/data/saxs_computation/mv/1mvk/1mvk.fit
pddf	/app/data/pr_computation/mv/1mvk/1mvk.pr.out
profile	/app/data/saxs_computation/mv/1mvk/1mvk.dat

X-ray structure of the tetrameric mutant of the B1 domain of streptococcal protein G

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 non-polymer

Entity 3 water

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)