1jmu

Crystal Structure of the Reovirus mu1/sigma3 Complex

Method: X-RAY DIFFRACTION D_max: 147.8 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	1jmu
沉积日期 deposition_date	2001-07-20
结构标题 title	Crystal Structure of the Reovirus mu1/sigma3 Complex
关键词 keywords	Protein-protein complex, jelly roll, zinc finger, Viral protein; VIRAL PROTEIN
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	45.14 Å
回转半径 Rg (电子) rg_electron	44.38 Å
零角强度 I(0) i0	1612900000.00
分子量 molecular_weight	333390.0 kDa
排除体积 excluded_volume	417130 Å³
包络体积 envelope_volume	518260 Å³
水化壳体积 shell_volume	93455 Å³
包络直径 envelope_diameter	152.4 Å
壳层 Rg shell_rg	51.61 Å
包络 Rg envelope_rg	44.33 Å
形状 Rg shape_rg	44.37 Å
总 Rg total_rg	44.66 Å
总原子数 total_atoms	23386
残基数 n_residues	3018
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	147.8 Å
Rg (实空间) rg_real	44.96 Å
Rg 误差 (实空间) rg_real_error	0.93 Å
I(0) (实空间) i0_real	1.6130e+09
I(0) 误差 (实空间) i0_real_error	2.5410e+07
Rg (倒空间) rg_reciprocal	45.14 Å
I(0) (倒空间) i0_reciprocal	1613000000.0000
解质量估计 total_estimate	0.8776
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	59.1 Å
偏度 Skewness skewness	0.240
峰度 Kurtosis kurtosis	-0.324
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	273000000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.867

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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 (8)

Entity 1 polymer

描述 description	PROTEIN MU-1
分子量 formula_weight	4050.4 kDa
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,C,E
原子数 atom_count	23657

GNASSIVQTINVTGDGNVFKPSAETSSTAVPSLSLSPGMLN

来源 Source

来源生物 organism	Reovirus sp.
NCBI 分类编号 ncbi_taxonomy_id	10891
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 polymer

描述 description	PROTEIN MU-1
分子量 formula_weight	72182.7 kDa
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	B,D,F

PGGVPWIAIGDETSVTSPGALRRMTSKDIPETAIINTDNSSGAVPSESALVPYNDEPLVVVTEHAIANFTKAEMALEFNREFLDKLRVLSVSPKYSDLLTYVDCYVGVSARQALNNFQKQVPVITPTRQTMYVDSIQAALKALEKWEIDLRVAQTLLPTNVPIGEVSCPMQSVVKLLDDQLPDDSLIRRYPKEAAVALAKRNGGIQWMDVSEGTVMNEAVNAVAASALAPSASAPPLEEKSKLTEQAMDLVTAAEPEIIASLVPVPAPVFAIPPKPADYNVRTLKIDEATWLRMIPKTMGTLFQIQVTDNTGTNWHFNLRGGTRVVNLDQIAPMRFVLDLGGKSYKETSWDPNGKKVGFIVFQSKIPFELWTAASQIGQATVVNYVQLYAEDSSFTAQSIIATTSLAYNYEPEQLNKTDPEMNYYLLATFIDSAAITPTNMTQPDVWDALLTMSPLSAGEVTVKGAVVSEVVPAELIGSYTPESLNASLPNDAARCMIDRASKIAEAIKIDDDAGPDEYSPNSVPIQGQLAISQLETGYGVRIFNPKGILSKIASRAMQAFIGDPSTIITQAAPVLSDKNNWIALAQGVKTSLRTKSLSAGVKTAVSKLSSSESIQNWTQGFLDKVSTHFPAPKPDCPTNGDGSEPSARRVKRDSYAGVVKRGYTR

来源 Source

来源生物 organism	Reovirus sp.
NCBI 分类编号 ncbi_taxonomy_id	10891
宿主生物 host_organism	Spodoptera frugiperda

Entity 3 polymer

描述 description	SIGMA 3 PROTEIN
分子量 formula_weight	41263.2 kDa
突变 mutation	A104C
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	G,H,I

XMEVCLPNGHQIVDLINNAFEGRVSIYSAQEGWDKTISAQPDMMVCGGAVVCMHCLGVVGSLQRKLKHLPHHRCNQQIRHQDYVDVQFADRVTAHWKRGMLSFVCQMHAMMNDVSPEDLDRVRTEGGSLVELNWLQVDPNSMFRSIHSSWTDPLQVVDDLDTKLDQYWTALNLMIDSSDLVPNFMMRDPSHAFNGVRLEGDARQTQFSRTFDSRSSLEWGVMVYDYSELEHDPSKGRAYRKELVTPARDFGHFGLSHYSRATTPILGKMPAVFSGMLTGNCKMYPFIKGTAKLKTVRKLVDSVNHAWGVEKIRYALGPGGMTGWYNRTMQQAPIVLTPAALTMFSDTTKFGDLDYPVMIGDPMILG

来源 Source

来源生物 organism	Reovirus sp.
NCBI 分类编号 ncbi_taxonomy_id	10891
宿主生物 host_organism	Spodoptera frugiperda

Entity 4 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	octyl beta-D-glucopyranoside
分子量 formula_weight	292.4 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 6 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	9

Entity 7 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 8 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	271

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1jmu.1
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.35 — Membrane penetration protein mu1
超家族 Superfamily superfamily	e.35.1 — Membrane penetration protein mu1
家族 Family family	e.35.1.1 — Membrane penetration protein mu1

结构域编号 domain_id	d1jmu.2
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.35 — Membrane penetration protein mu1
超家族 Superfamily superfamily	e.35.1 — Membrane penetration protein mu1
家族 Family family	e.35.1.1 — Membrane penetration protein mu1

结构域编号 domain_id	d1jmu.3
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.35 — Membrane penetration protein mu1
超家族 Superfamily superfamily	e.35.1 — Membrane penetration protein mu1
家族 Family family	e.35.1.1 — Membrane penetration protein mu1

结构域编号 domain_id	d1jmug_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.196 — Outer capsid protein sigma 3
超家族 Superfamily superfamily	d.196.1 — Outer capsid protein sigma 3
家族 Family family	d.196.1.1 — Outer capsid protein sigma 3

结构域编号 domain_id	d1jmuh_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.196 — Outer capsid protein sigma 3
超家族 Superfamily superfamily	d.196.1 — Outer capsid protein sigma 3
家族 Family family	d.196.1.1 — Outer capsid protein sigma 3

结构域编号 domain_id	d1jmui_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.196 — Outer capsid protein sigma 3
超家族 Superfamily superfamily	d.196.1 — Outer capsid protein sigma 3
家族 Family family	d.196.1.1 — Outer capsid protein sigma 3

CATH v4.4 (18 domains)

结构域编号 domain_id	1jmuB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1370 — Protein mu-1, chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Protein mu-1, chain B, domain 1

结构域编号 domain_id	1jmuB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	2040 — Protein mu-1, chain B, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Protein mu-1, chain B, domain 2

结构域编号 domain_id	1jmuB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	2050 — Protein mu-1, chain B, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Protein mu-1, chain B, domain 3

结构域编号 domain_id	1jmuB04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	420 — Membrane penetration protein mu1, Chain B, domain 4

结构域编号 domain_id	1jmuD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1370 — Protein mu-1, chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Protein mu-1, chain B, domain 1

结构域编号 domain_id	1jmuD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	2040 — Protein mu-1, chain B, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Protein mu-1, chain B, domain 2

结构域编号 domain_id	1jmuD03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	2050 — Protein mu-1, chain B, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Protein mu-1, chain B, domain 3

结构域编号 domain_id	1jmuD04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	420 — Membrane penetration protein mu1, Chain B, domain 4

结构域编号 domain_id	1jmuF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1370 — Protein mu-1, chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Protein mu-1, chain B, domain 1

结构域编号 domain_id	1jmuF02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	2040 — Protein mu-1, chain B, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Protein mu-1, chain B, domain 2

结构域编号 domain_id	1jmuF03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	2050 — Protein mu-1, chain B, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Protein mu-1, chain B, domain 3

结构域编号 domain_id	1jmuF04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	420 — Membrane penetration protein mu1, Chain B, domain 4

结构域编号 domain_id	1jmuG01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1630 — Outer-capsid protein sigma 3, small lobe
同源超家族 H-superfamily homologous superfamily	10 — Outer-capsid protein sigma 3, small lobe

结构域编号 domain_id	1jmuG02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1320 — Outer-capsid protein sigma 3, large lobe
同源超家族 H-superfamily homologous superfamily	10 — Outer-capsid protein sigma 3, large lobe

结构域编号 domain_id	1jmuH01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1630 — Outer-capsid protein sigma 3, small lobe
同源超家族 H-superfamily homologous superfamily	10 — Outer-capsid protein sigma 3, small lobe

结构域编号 domain_id	1jmuH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1320 — Outer-capsid protein sigma 3, large lobe
同源超家族 H-superfamily homologous superfamily	10 — Outer-capsid protein sigma 3, large lobe

结构域编号 domain_id	1jmuI01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1630 — Outer-capsid protein sigma 3, small lobe
同源超家族 H-superfamily homologous superfamily	10 — Outer-capsid protein sigma 3, small lobe

结构域编号 domain_id	1jmuI02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1320 — Outer-capsid protein sigma 3, large lobe
同源超家族 H-superfamily homologous superfamily	10 — Outer-capsid protein sigma 3, large lobe

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7. 引用文献 (1)

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晶胞边长 a length_a	180.294 Å
晶胞边长 b length_b	184.942 Å
晶胞边长 c length_c	284.324 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	24

空间群 space_group	I 2 2 2
空间群编号 int_tables_number	23
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	35.000 Å
R 因子 r_factor	0.2160
R_work r_work	0.2160
R_free r_free	0.2410

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

Crystal Structure of the Reovirus mu1/sigma3 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 (8)

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 non-polymer

Entity 7 non-polymer

Entity 8 water

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (6 domains)

CATH v4.4 (18 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)