9mof

Structure of the bacteriophage T4 portal-neck-tail connector complex

Method: ELECTRON MICROSCOPY D_max: 456.2 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9mof
沉积日期 deposition_date	2024-12-26
结构标题 title	Structure of the bacteriophage T4 portal-neck-tail connector complex
关键词 keywords	;bacteriophage T4, portal vertex, phage neck, tail terminator protein, tube terminator protein, asymmetric phage reconstruction, DNA retention, neck stopper protein, head completion proteins, VIRAL PROTEIN ;; VIRAL PROTEIN
实验方法 method	ELECTRON MICROSCOPY

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	— Å
回转半径 Rg (电子) rg_electron	166.00 Å
零角强度 I(0) i0	517050000000.00
分子量 molecular_weight	6170800.0 kDa
排除体积 excluded_volume	7715300 Å³
包络体积 envelope_volume	13183000 Å³
水化壳体积 shell_volume	660000 Å³
包络直径 envelope_diameter	529.4 Å
壳层 Rg shell_rg	133.50 Å
包络 Rg envelope_rg	162.50 Å
形状 Rg shape_rg	165.90 Å
总 Rg total_rg	166.00 Å
总原子数 total_atoms	435087
残基数 n_residues	56085
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	456.2 Å
Rg (实空间) rg_real	162.30 Å
Rg 误差 (实空间) rg_real_error	2.40 Å
I(0) (实空间) i0_real	5.0350e+11
I(0) 误差 (实空间) i0_real_error	1.3410e+10
Rg (倒空间) rg_reciprocal	129.30 Å
I(0) (倒空间) i0_reciprocal	442900000000.0000
解质量估计 total_estimate	0.8535
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	152.1 Å
偏度 Skewness skewness	0.323
峰度 Kurtosis kurtosis	-0.907
角度范围 angular_range	— – 0.0450 Å⁻¹
当前正则化参数 α current_alpha	1.2380
最高正则化参数 α highest_alpha	45550000000.0000
实空间数据点数 n_real_points	10
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.028; Oscil: 0.975; Stabil: 0.983; Sysdev: 1.000; Positv: 1.000; Valcen: 0.871; Smooth: 0.002

▶

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

▶

5. 实体与聚合体信息 (11)

Entity 1 polymer

描述 description	gp14, neck protein
分子量 formula_weight	29597.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	0,k,l,m,n,p
原子数 atom_count	435087

MATYDKNLFAKLENRTGYSQTNETEILNPYVNFNHYKNSQILADVLVAESIQMRGVECYYVPREYVSPDLIFGEDLKNKFTKAWKFAAYLNSFEGYEGAKSFFSNFGMQVQDEVTLSINPNLFKHQVNGKEPKEGDLIYFPMDNSLFEINWVEPYDPFYQLGQNAIRKITAGKFIYSGEEINPVLQKNEGINIPEFSELELNAVRNLNGIHDINIDQYAEVDQINSEAKEYVEPYVVVNNRGKSFESSPFDNDFMD

Entity 2 polymer

描述 description	gp18, tail sheath protein
分子量 formula_weight	71348.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	30

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1,2,3,4,5,AD,AK,AL,AM,AN,AO,AP,B1,B2,B3,B4,B5,B6,B7,Bp,Bq,Br,Bs,Bt,Bu,Bv,Bw,Bx,By,Bz

MTLLSPGIELKETTVQSTVVNNSTGTAALAGKFQWGPAFQIKQVTNEVDLVNTFGQPTAETADYFMSAMNFLQYGNDLRVVRAVDRDTAKNSSPIAGNIEYTISTPGSNYAVGDKITVKYVSDDIETEGKITEVDADGKIKKINIPTAKIIAKAKEVGEYPTLGSNWTAEISSSSSGLAAVITLGKIITDSGILLAEIENAEAAMTAVDFQANLKKYGIPGVVALYPGELGDKIEIEIVSKADYAKGASALLPIYPGGGTRASTAKAVFGYGPQTDSQYAIIVRRNDAIVQSVVLSTKRGGKDIYDSNIYIDDFFAKGGSEYIFATAQNWPEGFSGILTLSGGLSSNAEVTAGDLMEAWDFFADRESVDVQLFIAGSCAGESLETASTVQKHVVSIGDVRQDCLVLCSPPRETVVGIPVTRAVDNLVNWRTAAGSYTDNNFNISSTYAAIDGNYKYQYDKYNDVNRWVPLAADIAGLCARTDNVSQTWMSPAGYNRGQILNVIKLAIETRQAQRDRLYQEAINPVTGTGGDGYVLYGDKTATSVPSPFDRINVRRLFNMLKTNIGRSSKYRLFELNNAFTRSSFRTETAQYLQGIKALGGIYEYRVVCDTTNNTPSVIDRNEFVATFYIQPARSINYITLNFVATATGADFDELTGLAG

Entity 3 polymer

描述 description	gp19, tail tube protein
分子量 formula_weight	18479.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	30

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	6,7,8,9,AA,AE,AF,AG,AH,AI,AJ,BX,BY,BZ,Ba,Bb,Bc,Bd,Be,Bf,Bg,Bh,Bi,Bj,Bk,Bl,Bm,Bn,Bo,o

MFVDDVTRAFESGDFARPNLFQVEISYLGQNFTFQCKATALPAGIVEKIPVGFMNRKINVAGDRTFDDWTVTVMNDEAHDARQKFVDWQSIAAGQGNEITGGKPAEYKKSAIVRQYARDAKTVTKEIEIKGLWPTNVGELQLDWDSNNEIQTFEVTLALDYWE

Entity 4 polymer

描述 description	gpwac, fibritin
分子量 formula_weight	51909.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	36

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,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,a,b,c,d,e,f,g,h,i,j

MTDIVLNDLPFVDGPPAEGQSRISWIKNGEEILGADTQYGSEGSMNRPTVSVLRNVEVLDKNIGILKTSLETANSDIKTIQGILDVSGDIEALAQIGINKKDISDLKTLTSEHTEILNGTNNTVDSILADIGPFNAEANSVYRTIRNDLLWIKRELGQYTGQDINGLPVVGNPSSGMKHRIINNTDVITSQGIRLSELETKFIESDVGSLTIEVGNLREELGPKPPSFSQNVYSRLNEIDTKQTTVESDISAIKTSIGYPGNNSIITSVNTNTDNIASINLELNQSGGIKQRLTVIETSIGSDDIPSSIKGQIKDNTTSIESLNGIVGENTSSGLRANVSWLNQIVGTDSSGGQPSPPGSLLNRVSTIETSVSGLNNAVQNLQVEIGNNSAGIKGQVVALNTLVNGTNPNGSTVEERGLTNSIKANETNIASVTQEVNTAKGNISSLQGDVQALQEAGYIPEAPRDGQAYVRKDGEWVFLSTFLSPA

Entity 5 polymer

描述 description	gp20, portal protein
分子量 formula_weight	61117.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A0,A1,A2,A3,Av,Ax,BA,BB,BD,BF,BG,BH

MKFNVLSLFAPWAKMDERNFKDQEKEDLVSITAPKLDDGAREFEVSSNEAASPYNAAFQTIFGSYEPGMKTTRELIDTYRNLMNNYEVDNAVSEIVSDAIVYEDDTEVVALNLDKSKFSPKIKNMMLDEFSDVLNHLSFQRKGSDHFRRWYVDSRIFFHKIIDPKRPKEGIKELRRLDPRQVQYVREIITETEAGTKIVKGYKEYFIYDTAHESYACDGRMYEAGTKIKIPKAAVVYAHSGLVDCCGKNIIGYLHRAVKPANQLKLLEDAVVIYRITRAPDRRVWYVDTGNMPARKAAEHMQHVMNTMKNRVVYDASTGKIKNQQHNMSMTEDYWLQRRDGKAVTEVDTLPGADNTGNMEDIRWFRQALYMALRVPLSRIPQDQQGGVMFDSGTSITRDELTFAKFIRELQHKFEEVFLDPLKTNLLLKGIITEDEWNDEINNIKIEFHRDSYFAELKEAEILERRINMLTMAEPFIGKYISHRTAMKDILQMTDEEIEQEAKQIEEESKEARFQDPDQEQEDF

Entity 6 polymer

描述 description	gp23, major capsid protein
分子量 formula_weight	56074.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	30

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A4,A5,A7,A8,A9,AV,AW,AX,AZ,Ac,Ad,Ae,Af,Ag,Ah,Ai,Aj,Ak,Am,An,Ao,Ap,Au,Aw,Ay,Az,BI,BJ,BK,BM

MTIKTKAELLNKWKPLLEGEGLPEIANSKQAIIAKIFENQEKDFQTAPEYKDEKIAQAFGSFLTEAEIGGDHGYNATNIAAGQTSGAVTQIGPAVMGMVRRAIPNLIAFDICGVQPMNSPTGQVFALRAVYGKDPVAAGAKEAFHPMYGPDAMFSGQGAAKKFPALAASTQTTVGDIYTHFFQETGTVYLQASVQVTIDAGATDAAKLDAEIKKQMEAGALVEIAEGMATSIAELQEGFNGSTDNPWNEMGFRIDKQVIEAKSRQLKAAYSIELAQDLRAVHGMDADAELSGILATEIMLEINREVVDWINYSAQVGKSGMTLTPGSKAGVFDFQDPIDIRGARWAGESFKALLFQIDKEAVEIARQTGRGEGNFIIASRNVVNVLASVDTGISYAAQGLATGFSTDTTKSVFAGVLGGKYRVYIDQYAKQDYFTVGYKGPNEMDAGIYYAPYVALTPLRGSDPKNFQPVMGFKTRYGIGINPFAESAAQAPASRIQSGMPSILNSLGKNAYFRRVYVKGI

Entity 7 polymer

描述 description	gp13, neck protein
分子量 formula_weight	34772.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A6,AY,Aa,Ab,Al,Aq,Ar,As,At,BC,BE,BL

MSGYNPQNPKELKDVILRRLGAPIINVELTPDQIYDCIQRALELYGEYHFDGLNKGFHVFYVGDDEERYKTGVFDLRGSNVFAVTRILRTNIGSITSMDGNATYPWFTDFLLGMAGINGGMGTSCNRFYGPNAFGADLGYFTQLTSYMGMMQDMLSPIPDFWFNSANEQLKVMGNFQKYDLIIVESWTKSYIDTNKMVGNTVGYGTVGPQDSWSLSERYNNPDHNLVGRVVGQDPNVKQGAYNNRWVKDYATALAKELNGQILARHQGMMLPGGVTIDGQRLIEEARLEKEALREELYLLDPPFGILVG

Entity 8 polymer

描述 description	gp15, tail terminator protein
分子量 formula_weight	31587.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	AB,q,r,s,t,u

MFGYFYNSSFRRYATLMGDLFSNIQIKRQLESGDKFIRVPITYASKEHFMMKLNKWTSINSQEDVAKVETILPRINLHLVDFSYNAPFKTNILNQNLLQKGATSVVSQYNPSPIKMIYELSIFTRYEDDMFQIVEQILPYFQPHFNTTMYEQFGNDIPFKRDIKIVLMSAAIDEAIDGDNLSRRRIEWSLTFEVNGWMYPPVDDAEGLIRTTYTDFHANTRDLPDGEGVFESVDSEVVPRDIDPEDWDGTVKQTFTSNVNRPTPPEPPGPRT

Entity 9 polymer

描述 description	gp3, tube terminator protein
分子量 formula_weight	19723.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	AC,v,w,x,y,z

MSQALQQIFNQANTTNFVVSIPHSNTTSAFTLNAQSVPIPGIRIPVTDTVTGPFGLGRAQRPGVTFEYDPLIVRFIVDEELKSWIGMYEWMLGTSNYLTGENTAQKTGPEYITLYILDNSKTEIVMSINFYKPWVSDLSEVEFSYTEDSDPALVCTATIPYTYFQVEKDGKIIAEV

Entity 10 polymer

描述 description	Hoc, highly immunogenic outer capsid protein
分子量 formula_weight	40416.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	AQ,AR,AS,AT,AU

MTFTVDITPKTPTGVIDETKQFTATPSGQTGGGTITYAWSVDNVPQDGAEATFSYVLKGPAGQKTIKVVATNTLSEGGPETAEATTTITVKNKTQTTTLAVTPASPAAGVIGTPVQFTAALASQPDGASATYQWYVDDSQVGGETNSTFSYTPTTSGVKRIKCVAQVTATDYDALSVTSNEVSLTVNKKTMNPQVTLTPPSINVQQDASATFTANVTGAPEEAQITYSWKKDSSPVEGSTNVYTVDTSSVGSQTIEVTATVTAADYNPVTVTKTGNVTVTAKVAPEPEGELPYVHPLPHRSSAYIWCGWWVMDEIQKMTEEGKDWKTDDPDSKYYLHRYTLQKMMKDYPEVDVQESRNGYIIHKTALETGIIYTYP

Entity 11 polymer

描述 description	Soc, small outer capsid protein
分子量 formula_weight	9129.1 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	BN,BO,BP,BQ,BR,BS,BT,BU,BV,BW

MASTRGYVNIKTFEQKLDGNKKIEGKEISVAFPLYSDVHKISGAHYQTFPSEKAAYSTVYEENQRTEWIAANEDLWKVTG

▶

7. 引用文献 (1)

▶

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	—

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

分辨率 resolution	3.80 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	69000

fit	/app/data/saxs_computation/mo/9mof/9mof.fit
pddf	/app/data/pr_computation/mo/9mof/9mof.pr.out
profile	/app/data/saxs_computation/mo/9mof/9mof.dat

Structure of the bacteriophage T4 portal-neck-tail connector 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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (11)

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

Entity 7 polymer

聚合体 Polymer

Entity 8 polymer

聚合体 Polymer

Entity 9 polymer

聚合体 Polymer

Entity 10 polymer

聚合体 Polymer

Entity 11 polymer

聚合体 Polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)