SAXSdb — 2cse

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2cse
沉积日期 deposition_date	2005-05-21
结构标题 title	Features of Reovirus Outer-Capsid Protein mu1 Revealed by Electron and Image Reconstruction of the virion at 7.0-A Resolution
关键词 keywords	cryoEM, image processing, reovirus, membrane penetration protein, Icosahedral virus, Virus; VIRUS
实验方法 method	ELECTRON MICROSCOPY

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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	91.15 Å
回转半径 Rg (电子) rg_electron	90.82 Å
零角强度 I(0) i0	43405900000.00
分子量 molecular_weight	1783100.0 kDa
排除体积 excluded_volume	2185000 Å³
包络体积 envelope_volume	2708500 Å³
水化壳体积 shell_volume	249490 Å³
包络直径 envelope_diameter	306.4 Å
壳层 Rg shell_rg	89.94 Å
包络 Rg envelope_rg	86.91 Å
形状 Rg shape_rg	90.52 Å
总 Rg total_rg	90.82 Å
总原子数 total_atoms	—
残基数 n_residues	—
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	239.2 Å
Rg (实空间) rg_real	87.93 Å
Rg 误差 (实空间) rg_real_error	0.58 Å
I(0) (实空间) i0_real	4.1540e+10
I(0) 误差 (实空间) i0_real_error	8.2340e+08
Rg (倒空间) rg_reciprocal	91.28 Å
I(0) (倒空间) i0_reciprocal	43420000000.0000
解质量估计 total_estimate	0.9127
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	98.5 Å
偏度 Skewness skewness	0.174
峰度 Kurtosis kurtosis	-0.608
角度范围 angular_range	— – 0.0850 Å⁻¹
当前正则化参数 α current_alpha	0.8444
最高正则化参数 α highest_alpha	3053000000.0000
实空间数据点数 n_real_points	18
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 1.000; Stabil: 0.956; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; 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	major outer-capsid protein mu1
分子量 formula_weight	76346.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	10

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,P,Q,R,J,K,L,T
原子数 atom_count	16111

MGNASSIVQTINVTGDGNVFKPSAETSSTAVPSLSLSPGMLNPGGVPWIAIGDETSVTSPGALRRMTSKDIPETAIINTDNSSGAVPSESALVPYNDEPLVVVTEHAIANFTKAEMALEFNREFLDKLRVLSVSPKYSDLLTYVDCYVGVSARQALNNFQKQVPVITPTRQTMYVDSIQAALKALEKWEIDLRVAQTLLPTNVPIGEVSCPMQSVVKLLDDQLPDDSLIRRYPKEAAVALAKRNGGIQWMDVSEGTVMNEAVNAVAASALAPSASAPPLEEKSKLTEQAMDLVTAAEPEIIASLVPVPAPVFAIPPKPADYNVRTLKIDEATWLRMIPKTMGTLFQIQVTDNTGTNWHFNLRGGTRVVNLDQIAPMRFVLDLGGKSYKETSWDPNGKKVGFIVFQSKIPFELWTAASQIGQATVVNYVQLYAEDSSFTAQSIIATTSLAYNYEPEQLNKTDPEMNYYLLATFIDSAAITPTNMTQPDVWDALLTMSPLSAGEVTVKGAVVSEVVPAELIGSYTPESLNASLPNDAARCMIDRASKIAEAIKIDDDAGPDEYSPNSVPIQGQLAISQLETGYGVRIFNPKGILSKIASRAMQAFIGDPSTIITQAAPVLSDKNNWIALAQGVKTSLRTKSLSAGVKTAVSKLSSSESIQNWTQGFLDKVSTHFPAPKPDCPTNGDGSEPSARRVKRDSYAGVVKRGYTR

Entity 2 polymer

描述 description	major capsid surface protein sigma-3
分子量 formula_weight	41237.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	10

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	S,D,E,F,M,N,O,G,H,I

MEVCLPNGHQIVDLINNAFEGRVSIYSAQEGWDKTISAQPDMMVCGGAVVCMHCLGVVGSLQRKLKHLPHHRCNQQIRHQDYVDVQFADRVTAHWKRGMLSFVCQMHAMMNDVSPEDLDRVRTEGGSLVELNWLQVDPNSMFRSIHSSWTDPLQVVDDLDTKLDQYWTALNLMIDSSDLVPNFMMRDPSHAFNGVRLEGDARQTQFSRTFDSRSSLEWGVMVYDYSELEHDPSKGRAYRKELVTPARDFGHFGLSHYSRATTPILGKMPAVFSGMLTGNCKMYPFIKGTAKLKTVRKLVDSVNHAWGVEKIRYALGPGGMTGWYNRTMQQAPIVLTPAALTMFSDTTKFGDLDYPVMIGDPMILG

Entity 3 polymer

描述 description	guanylyltransferase
分子量 formula_weight	144098.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	U

MANVWGVRLADSLSSPTIETRTRQYTLHDLCSDLDANPGREPWKPLRNQRTNNIVAVQLFRPLQGLVLDTQLYGFPGAFDDWERFMREKLRVLKYEVLRIYPISNYSNEHVNVFVANALVGAFLSNQAFYDLLPLLIINDTMIGDLLGTGASLSQFFQSHGDVLEVAAGRKYLQMENYSNDDDDPPLFAKDLSDYAKAFYSDTYEVLDRFFWTHDSSAGVLVHYDKPTNGHHYLLGTLTQMVSAPPYIINATDAMLLESCLEQFSANVRARPAQPVTRLDQCYHLRWGAQYVGEDSLTYRLGVLSLLATNGYQLARPIPRQLTNRWLSSFVSQIMSDGVNETPLWPQERYVQIAYDSPSVVDGATQYGYVRKNQLRLGMRISALQSLSDTPSPVQWLPQYTIDQAAMDEGDLMVSRLTQLPLRPDYGNIWVGDALSYYVDYNRSHRVVLSSELPQLPDTYFDGDEQYGRSLFSLARKIGDRSLVKDTAVLKHAYQAIDPNTGKEYLRSRQSVAYFGASAGHSGADQPLVIEPWIQGKISGVPPPSSVRQFGYDVARGAIVDLARPFPSGDYQFVYSDVDQVVDGHDDLSISSGLVESLLSSCMHATAPGGSFVVKINFPTRPVWHYIEQKILPNITSYMLIKPFVTNNVELFFVAFGVHQHSSLTWTSGVYFFLVDHFYRYETLSTISRQLPSFGYVDDGSSVTGIETISIENPGFSNMTQAARIGISGLCANVGNARKSIAIYESHGARVLTITSRRSPASARRKSRLRYLPLIDPRSLEVQARTILPADPVLFENVSGASPHVCLTMMYNFEVSSAVYDGDVVLDLGTGPEAKILELIPATSPVTCVDIRPTAQPSGCWNVRTTFLELDYLSDGWITGVRGDIVTCMLSLGAAAAGKSMTFDAAFQQLIKVLSKSTANVVLVQVNCPTDVVRSIKGYLEIDSTNKRYRFPKFGRDEPYSDMDALEKICRTAWPNCSITWVPLSYDLRWTRLALLESTTLSSASIRIAELMYKYMPIMRIDIHGLPMEKRGNFIVGQNCSLVIPGFNAQDVFNCYFNSALAFSTEDVNAAMIPQVSAQFDATKGEWTLDMVFSDAGIYTMQALVGSNANPVSLGSFVVDSPDVDITDAWPAQLDFTIAGTDVDITVNPYYRLMTFVRIDGQWQIANPDKFQFFSSASGTLVMNVKLDIADKYLLYYIRDVQSRDVGFYIQHPLQLLNTITLPTNEDLFLSAPDMREWAVKESGNTICILNSQGFVLPQDWDVLTDTISWSPSIPTYIVPPGDYTLTPL

Entity 4 polymer

描述 description	major core protein lambda 1
分子量 formula_weight	142008.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	V,W

MKRIPRKTKGKSSGKGNDSTERSDDGSSQLRDKQNNKAGPATTEPGTSNREQYRARPGIASVQRATESAELPMKNNDEGTPDKKGNTRGDLVNEHSEAKDEADEATQKQAKDTDKSKAQVTYSDTGINNANELSRSGNVDNEGGSNQKPMSTRIAEATSAIVSKHPARVGLPPTASSGHGYQCHVCSAVLFSPLDLDAHVASHGLHGNMTLTSSEIQRHITEFISSWQNHPIVQVSADVENKKTAQLLHADTPRLVTWDAGLCTSFKIVPIVPAQVPQDVLAYTFFTSSYAIQSPFPEAAVSRIVVHTRWASNVDFDRDSSVIMAPPTENNIHLFKQLLNTETLSVRGANPLMFRANVLHMLLEFVLDNLYLNRHTGFSQDHTPFTEGANLRSLPGPDAEKWYSIMYPTRMGTPNVSKICNFVASCVRNRVGRFDRAQMMNGAMSEWVDVFETSDALTVSIRGRWMARLARMNINPTEIEWALTECAQGYVTVTSPYAPSVNRLMPYRISNAERQISQIIRIMNIGNNATVIQPVLQDISVLLQRISPLQIDPTIISNTMSTVSESTTQTLSPASSILGKLRPSNSDFSSFRVALAGWLYNGVVTTVIDDSSYPKDGGSVTSLENLWDFFILALALPLTTDPCAPVKAFMTLANMMVGFETIPMDNQIYTQSRRASAFSTPHTWPRCFMNIQLISPIDAPILRQWAEIIHRYWPNPSQIRYGAPNVFGSANLFTPPEVLLLPIDHQPANVTTPTLDFTNELTNWRARVCELMKNLVDNQRYQPGWTQSLVSSMRGTLDKLKLIKSMTPMYLQQLAPVELAVIAPMLPFPPFQVPYVRLDRDRVPTMVGVTRQSRDTITQPALSLSTTNTTVGVPLALDARAITVALLSGKYPPDLVTNVWYADAIYPMYADTEVFSNLQRDMITCEAVQTLVTLVAQISETQYPVDRYLDWIPSLRASAATAATFAEWVNTSMKTAFDLSDMLLEPLLSGDPRMTQLAIQYQQYNGRTFNVIPEMPGSVIADCVQLTAEVFNHEYNLFGIARGDIIIGRVQSTHLWSPLAPPPDLVFDRDTPGVHIFGRDCRISFGMNGAAPMIRDETGMMVPFEGNWIFPLALWQMNTRYFNQQFDAWIKTGELRIRIEMGAYPYMLHYYDPRQYANAWNLTSAWLEEITPTSIPSVPFMVPISSDHDISSAPAVQYIISTEYNDRSLFCTNSSSPQTIAGPDKHIPVERYNILTNPDAPPTQIQLPEVVDLYNVVTRYAYETPPITAVVMGVP

Entity 5 polymer

描述 description	Sigma 2 protein
分子量 formula_weight	47155.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	X,Y,Z

MARAAFLFKTVGFGGLQNVPINDELSSHLLRAGNSPWQLTQFLDWISLGRGLATSALVPTAGSRYYQMSCLLSGTLQIPFRPNHRWGDIRFLRLVWSAPTLDGLVVAPPQVLAQPALQAQADRVYDCDDYPFLARDPRFKHRVYQQLSAVTLLNLTGFGPISYVRVDEDMWSGDVNQLLMNYFGHTFAEIAYTLCQASANRPWEHDGTYARMTQIILSLFWLSYVGVIHQQNTYRTFYFQCNRRGDAAEVWILSCSLNHSAQIRPGNRSLFVMPTSPDWNMDVNLILSSTLTGCLCSGSQLPLIDNNSVPAVSRNIHGWTGRAGNQLHGFQVRRMVTEFCDRLRRDGVMTQAQQNQIEALADQTQQFKRDKLEAWAREDDQYNQANPNSTMFRTKPFTNAQWGRGNTGATSAAIAALI

Entity 6 polymer

描述 description	Minor core protein lambda 3
分子量 formula_weight	142510.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1

MSSMILTQFRPFIESISGITDQSNDVFEDAAKAFSMFTRSDVYKALDEIPFSDDAMLPIPPTIYTKPSHDSYYYIDALNRVRRKTYQGPDDVYVPNCSIVELLEPHETLTSYGRLSEAIENRAKDGDSQARIATTYGRIAESQARQIKAPLEKFVLALLVSEAGGSLYDPVLQKYDEIPDLSHNCPLWCFREICRHISGPLPDRAPYLYLSAGVFWLMSPRMTSAIPPLLSDLVNLAILQQTAGLDPSLVKLGVQICLHAAASSSYAWFILKTKSIFPQNTLHSMYESLEGGYCPNLEWLEPRSDYKFMYMGVMPLSTKYARSAPSNDKKARELGEKYGLSSVVSELRKRTKTYVKHDFASVRYIRDAMACTSGIFLVRTPTETVLQEYTQSPEIKVPIPQKDWTGPVGEIRILKDTTSSIARYLYRTWYLAAARMAAQPRTWDPLFQAIMRSQYVTARGGSGAALRESLYAINVSLPDFKGLPVKAATKIFQAAQLANLPFSHTSVAILADTSMGLRNQVQRRPRSIMPLNVPQQQVSAPHTLTADYINYHMNLSTTSGSAVIEKVIPLGVYASSPPNQSINIDISACDASITWDFFLSVIMAAIHEGVASGSIGKPFMGVPASIVNDESVVGVRAARPISGMQNMIQHLSKLYKRGFSYRVNDSFSPGNDFTHMTTTFPSGSTATSTEHTANNSTMMETFLTVWGPEHTDDPDVLRLMKSLTIQRNYVCQGDDGLMIIDGNTAGKVNSETIQKMLELISKYGEEFGWKYDIAYDGTAEYLKLYFIFGCRIPNLSRHPIVGKERANSSAEEPWPAILDQIMGIFFNGVHDGLQWQRWIRYSWALCCAFSRQRTMIGESVGYLQYPMWSFVYWGLPLVKVFGSDPWIFSWYMPTGDLGMYSWISLIRPLMTRWMVANGYATDRCSPVFGNADYRRCFNEIKLYQGYYMAQLPRNPTKSGRAAPREVREQFTQALSDYLMQNPELKSRVLRGRSEWEKYGAGIIHNPPSLFDVPHKWYLGAQEAATATREELAEMDETLMRARRHSYSSFSKLLEAYLLVKWRMCEAREPSVDLRLPLCAGIDPLNSDPFLKMVSVGPMLQSTRKYFAQTLFMAKTVSGLDVNAIDSALLRLRTLGADKKALTAQLLMVGLQESEADALAGKIMLQDVSTVQLARVVNLAVPDTWMSLDFDSMFKHHVKLLPKDGRHLNTDIPPRMGWLRAILRFLGAGMVMTATGVAVDIYLEDIHGGGRALGQRFMTWMRQEGRSA

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6. 折叠分类 (SCOP + CATH) 11 domains

SCOP 2.08 (11 domains)

结构域编号 domain_id	d2csed1
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	d2csee1
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	d2csef1
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	d2cseg1
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	d2cseh1
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	d2csei1
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	d2csem1
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	d2csen1
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	d2cseo1
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	d2cses1
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	d2cseu1
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.7 — Reovirus components
超家族 Superfamily superfamily	i.7.1 — Reovirus components
家族 Family family	i.7.1.1 — Reovirus components

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	1

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	7.00 Å
分辨率测定方法 resolution_method	PFT, OOR, POR
颗粒数 num_particles	7939

fit	/app/data/saxs_computation/cs/2cse/2cse.fit
pddf	/app/data/pr_computation/cs/2cse/2cse.pr.out
profile	/app/data/saxs_computation/cs/2cse/2cse.dat

Features of Reovirus Outer-Capsid Protein mu1 Revealed by Electron and Image Reconstruction of the virion at 7.0-A Resolution

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (6)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

Entity 6 polymer

聚合体 Polymer

6. 折叠分类 (SCOP + CATH) 11 domains

SCOP 2.08 (11 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)