SAXSdb — 2hzm

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2hzm
沉积日期 deposition_date	2006-08-09
结构标题 title	Structure of the Mediator head subcomplex Med18/20
关键词 keywords	beta barrel, channel, TRANSCRIPTION; TRANSCRIPTION
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	46.39 Å
回转半径 Rg (电子) rg_electron	46.36 Å
零角强度 I(0) i0	505890000.00
分子量 molecular_weight	189900.0 kDa
排除体积 excluded_volume	239880 Å³
包络体积 envelope_volume	341640 Å³
水化壳体积 shell_volume	64840 Å³
包络直径 envelope_diameter	166.7 Å
壳层 Rg shell_rg	47.43 Å
包络 Rg envelope_rg	46.17 Å
形状 Rg shape_rg	46.35 Å
总 Rg total_rg	46.45 Å
总原子数 total_atoms	13358
残基数 n_residues	1717
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	161.9 Å
Rg (实空间) rg_real	46.59 Å
Rg 误差 (实空间) rg_real_error	1.85 Å
I(0) (实空间) i0_real	5.0590e+08
I(0) 误差 (实空间) i0_real_error	1.0100e+07
Rg (倒空间) rg_reciprocal	46.39 Å
I(0) (倒空间) i0_reciprocal	505800000.0000
解质量估计 total_estimate	0.8568
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	52.4 Å
偏度 Skewness skewness	0.448
峰度 Kurtosis kurtosis	-0.194
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	30470000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.810; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.713

▶

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

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	RNA polymerase II mediator complex subunit 20
分子量 formula_weight	23076.2 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,E,G
原子数 atom_count	13587

ASMGKSAVIFVERATPATLTELKDALSNSILSVRDPWSIDFRTYRCSIKNLPADVSKLMYSITFHHHGRQTVLIKDNSAMVTTAAAADIPPALVFNGSSTGVPESIDTILSSKLSNIWMQRQLIKGDAGETLILDGLTVRLVNLFSSTGFKGLLIELQADEAGEFETKIAGIEGHLAEIRAKEYKTSSDSLGPDTSNEICDLAYQYVRALEL

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	RNA polymerase II mediator complex subunit 18
分子量 formula_weight	35497.8 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

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

VQQLSLFGSIGDDGYDLLISTLTTISGNPPLLYNSLCTVWKPNPSYDVENVNSRNQLVEPNRIKLSKEVPFSYLIDETMMDKPLNFRILKSFTNDKIPLNYAMTRNILHNTVPQVTNFNSTNEDQNNSKHTEDTVNESRNSDDIIDVDMDASPAPSNESCSPWSLQISDIPAAGNNRSVSMQTIAETIILSSAGKNSSVSSLMNGLGYVFEFQYLTIGVKFFMKHGLILELQKIWQIEEAGNSQITSGGFLLKAYINVSRGTDIDRINYTETVLMNLKKELQGYIELSVPDRQSMDSRVAHGNILIAAALEHHHHHH

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	229

▼

6. 折叠分类 (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

结构域编号 domain_id	2hzmA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	310 — TATA-Binding Protein
同源超家族 H-superfamily homologous superfamily	180 —

结构域编号 domain_id	2hzmA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	140 — q64v53_bacfr protein fold
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2hzmB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	320 — Hypothetical Protein Pfu-838710-001
同源超家族 H-superfamily homologous superfamily	10 — Hypothetical Protein Pfu-838710-001

结构域编号 domain_id	2hzmC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	310 — TATA-Binding Protein
同源超家族 H-superfamily homologous superfamily	180 —

结构域编号 domain_id	2hzmC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	140 — q64v53_bacfr protein fold
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2hzmD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	320 — Hypothetical Protein Pfu-838710-001
同源超家族 H-superfamily homologous superfamily	10 — Hypothetical Protein Pfu-838710-001

结构域编号 domain_id	2hzmE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	310 — TATA-Binding Protein
同源超家族 H-superfamily homologous superfamily	180 —

结构域编号 domain_id	2hzmE02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	140 — q64v53_bacfr protein fold
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2hzmF00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	320 — Hypothetical Protein Pfu-838710-001
同源超家族 H-superfamily homologous superfamily	10 — Hypothetical Protein Pfu-838710-001

结构域编号 domain_id	2hzmG01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	310 — TATA-Binding Protein
同源超家族 H-superfamily homologous superfamily	180 —

结构域编号 domain_id	2hzmG02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	140 — q64v53_bacfr protein fold
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2hzmH00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	320 — Hypothetical Protein Pfu-838710-001
同源超家族 H-superfamily homologous superfamily	10 — Hypothetical Protein Pfu-838710-001

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	72.903 Å
晶胞边长 b length_b	129.352 Å
晶胞边长 c length_c	241.725 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	16

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2280
R_work r_work	0.2280
R_free r_free	0.2640

fit	/app/data/saxs_computation/hz/2hzm/2hzm.fit
pddf	/app/data/pr_computation/hz/2hzm/2hzm.pr.out
profile	/app/data/saxs_computation/hz/2hzm/2hzm.dat

Structure of the Mediator head subcomplex Med18/20

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)