1yar

Structure of Archeabacterial 20S proteasome mutant D9S- PA26 complex

Method: X-RAY DIFFRACTION D_max: 176.0 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	1yar
沉积日期 deposition_date	2004-12-17
结构标题 title	Structure of Archeabacterial 20S proteasome mutant D9S- PA26 complex
关键词 keywords	proteasome 20S, PA26 proteasome activator 11S, HYDROLASE-HYDROLASE ACTIVATOR COMPLEX; HYDROLASE/HYDROLASE ACTIVATOR
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	53.77 Å
回转半径 Rg (电子) rg_electron	53.32 Å
零角强度 I(0) i0	3447880000.00
分子量 molecular_weight	496530.0 kDa
排除体积 excluded_volume	623990 Å³
包络体积 envelope_volume	867220 Å³
水化壳体积 shell_volume	131370 Å³
包络直径 envelope_diameter	167.1 Å
壳层 Rg shell_rg	60.65 Å
包络 Rg envelope_rg	51.55 Å
形状 Rg shape_rg	53.30 Å
总 Rg total_rg	53.57 Å
总原子数 total_atoms	34839
残基数 n_residues	4494
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	176.0 Å
Rg (实空间) rg_real	53.57 Å
Rg 误差 (实空间) rg_real_error	1.10 Å
I(0) (实空间) i0_real	3.4480e+09
I(0) 误差 (实空间) i0_real_error	6.7350e+07
Rg (倒空间) rg_reciprocal	53.92 Å
I(0) (倒空间) i0_reciprocal	3450000000.0000
解质量估计 total_estimate	0.8043
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	66.8 Å
偏度 Skewness skewness	0.220
峰度 Kurtosis kurtosis	-0.362
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	267400000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.830; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.000

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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 (6)

Entity 1 polymer

描述 description	Proteasome alpha subunit
分子量 formula_weight	25801.4 kDa
EC 编号 ec_number	3.4.25.1
突变 mutation	D9S
来源方法 src_method	man
拷贝数 entity_count	7

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G
原子数 atom_count	39593

MQQGQMAYSRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQNSIEKIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAGIDQIGPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKENLPEKEAVTLGIKALKSSLEEGEELKAPEIASITVGNKYRIYDQEEVKKFL

来源 Source

来源生物 organism	Thermoplasma acidophilum
NCBI 分类编号 ncbi_taxonomy_id	2303
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	Proteasome beta subunit
分子量 formula_weight	23998.7 kDa
EC 编号 ec_number	3.4.25.1
来源方法 src_method	man
拷贝数 entity_count	7

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H,I,J,K,L,M,N

MNQTLETGTTTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAELELYRLQRRVNMPIEAVATLLSNMLNQVKYMPYMVQLLVGGIDTAPHVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQYSEKMTVDEGVDLVIRAISAAKQRDSASGGMIDVAVITRKDGYVQLPTDQIESRIRKLGLILHHHHHH

来源 Source

来源生物 organism	Thermoplasma acidophilum
NCBI 分类编号 ncbi_taxonomy_id	2303
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

描述 description	proteasome activator protein PA26
分子量 formula_weight	26087.6 kDa
来源方法 src_method	man
拷贝数 entity_count	7

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	O,P,Q,R,S,T,U

MHHHHHHPPKRAALIQNLRDSYTETSSFAVIEEWAAGTLQEIEGIAKAAAEAHGVIRNSTYGRAQAEKSPEQLLGVLQRYQDLCHNVYCQAETIRTVIAIRIPEHKEEDNLGVAVQHAVLKIIDELEIKTLGSGEKSGSGGAPTPIGMYALREYLSARSTVEDKLLGSVDAESGKTKGGSQSPSLLLELRQIDADFMLKVELATTHLSTMVRAVINAYLLNWKKLIQPRTGSDHMVS

来源 Source

来源生物 organism	Trypanosoma brucei
NCBI 分类编号 ncbi_taxonomy_id	5691
宿主生物 host_organism	Escherichia coli BL21(DE3)

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	21

Entity 5 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

Entity 6 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	3470

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6. 折叠分类 (SCOP + CATH) 42 domains

SCOP 2.08 (21 domains)

结构域编号 domain_id	d1yara_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.4 — Proteasome subunits

结构域编号 domain_id	d1yarb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.4 — Proteasome subunits

结构域编号 domain_id	d1yarc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.4 — Proteasome subunits

结构域编号 domain_id	d1yard_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.4 — Proteasome subunits

结构域编号 domain_id	d1yare_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.4 — Proteasome subunits

结构域编号 domain_id	d1yarf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.4 — Proteasome subunits

结构域编号 domain_id	d1yarg_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.4 — Proteasome subunits

结构域编号 domain_id	d1yarh_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.4 — Proteasome subunits

结构域编号 domain_id	d1yari_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.4 — Proteasome subunits

结构域编号 domain_id	d1yarj_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.4 — Proteasome subunits

结构域编号 domain_id	d1yark_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.4 — Proteasome subunits

结构域编号 domain_id	d1yarl_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.4 — Proteasome subunits

结构域编号 domain_id	d1yarm_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.4 — Proteasome subunits

结构域编号 domain_id	d1yarn_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.4 — Proteasome subunits

结构域编号 domain_id	d1yaro_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.8 — Proteasome activator
家族 Family family	a.24.8.1 — Proteasome activator

结构域编号 domain_id	d1yarp_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.8 — Proteasome activator
家族 Family family	a.24.8.1 — Proteasome activator

结构域编号 domain_id	d1yarq_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.8 — Proteasome activator
家族 Family family	a.24.8.1 — Proteasome activator

结构域编号 domain_id	d1yarr_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.8 — Proteasome activator
家族 Family family	a.24.8.1 — Proteasome activator

结构域编号 domain_id	d1yars_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.8 — Proteasome activator
家族 Family family	a.24.8.1 — Proteasome activator

结构域编号 domain_id	d1yart_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.8 — Proteasome activator
家族 Family family	a.24.8.1 — Proteasome activator

结构域编号 domain_id	d1yaru_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.8 — Proteasome activator
家族 Family family	a.24.8.1 — Proteasome activator

CATH v4.4 (21 domains)

结构域编号 domain_id	1yarA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1yarB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1yarC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1yarD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1yarE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1yarF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1yarG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1yarH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1yarI00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1yarJ00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1yarK00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1yarL00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1yarM00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1yarN00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1yarO01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	180 — Proteasome activator pa28, C-terminal domain

结构域编号 domain_id	1yarP01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	180 — Proteasome activator pa28, C-terminal domain

结构域编号 domain_id	1yarQ01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	180 — Proteasome activator pa28, C-terminal domain

结构域编号 domain_id	1yarR01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	180 — Proteasome activator pa28, C-terminal domain

结构域编号 domain_id	1yarS01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	180 — Proteasome activator pa28, C-terminal domain

结构域编号 domain_id	1yarT01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	180 — Proteasome activator pa28, C-terminal domain

结构域编号 domain_id	1yarU01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	180 — Proteasome activator pa28, C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	254.874 Å
晶胞边长 b length_b	127.512 Å
晶胞边长 c length_c	181.182 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	92.45 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	28

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	1.900 Å
最低分辨率 resolution_low	47.300 Å
R 因子 r_factor	0.1820
R_work r_work	0.1819
R_free r_free	0.2162

Structure of Archeabacterial 20S proteasome mutant D9S- PA26 complex

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 (6)

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

来源 Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 42 domains

SCOP 2.08 (21 domains)

CATH v4.4 (21 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/ya/1yar/1yar.fit
pddf	/app/data/pr_computation/ya/1yar/1yar.pr.out
profile	/app/data/saxs_computation/ya/1yar/1yar.dat