8fqc

Structure of baseplate with receptor binding complex of Agrobacterium phage Milano

Method: ELECTRON MICROSCOPY D_max: 213.8 Å Quality: EXCELLENT

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	8fqc
沉积日期 deposition_date	2023-01-05
结构标题 title	Structure of baseplate with receptor binding complex of Agrobacterium phage Milano
关键词 keywords	Myophage, redox trigger, disulfides, 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	79.28 Å
回转半径 Rg (电子) rg_electron	79.18 Å
零角强度 I(0) i0	12822900000.00
分子量 molecular_weight	940520.0 kDa
排除体积 excluded_volume	1166800 Å³
包络体积 envelope_volume	1968500 Å³
水化壳体积 shell_volume	208340 Å³
包络直径 envelope_diameter	286.9 Å
壳层 Rg shell_rg	77.38 Å
包络 Rg envelope_rg	77.75 Å
形状 Rg shape_rg	79.15 Å
总 Rg total_rg	79.28 Å
总原子数 total_atoms	66089
残基数 n_residues	8728
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	213.8 Å
Rg (实空间) rg_real	75.60 Å
Rg 误差 (实空间) rg_real_error	0.59 Å
I(0) (实空间) i0_real	1.2290e+10
I(0) 误差 (实空间) i0_real_error	2.3010e+08
Rg (倒空间) rg_reciprocal	78.77 Å
I(0) (倒空间) i0_reciprocal	12810000000.0000
解质量估计 total_estimate	0.9167
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	85.5 Å
偏度 Skewness skewness	0.263
峰度 Kurtosis kurtosis	-0.453
角度范围 angular_range	— – 0.1000 Å⁻¹
当前正则化参数 α current_alpha	0.4949
最高正则化参数 α highest_alpha	1249000000.0000
实空间数据点数 n_real_points	21
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.991; Stabil: 0.987; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.015

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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 (11)

Entity 1 polymer

描述 description	Baseplate hub protein, gp26
分子量 formula_weight	49701.8 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	C1
原子数 atom_count	66089

MIKPMRIFIGGEELVTYTSAQLQRTKKQMTGSLTVEIFLDYVPTKPTIVNAVRGKEILVYIMGELAFTGIIDKRRGKSVKKQNRDASGRFAFSGGPGSLSEDAGGDVSVNFSKGNGYSVTLTARGRTKYLIDSSQTHPTGFFKNTSDKKVIETLVKEHNVVLQWDAEEIDEPKVTLRDGNRIYNEIFERCNQNCHFAYETRDGKLLITDGTNGTVGEDIILGYNILDFSAEQSEDQANSQITVKGHRTQKGVWGNDAIVQPVQTVADSWVGANIPLTIQHYGDATNEGLQRRAKFEADRRAAESKSVSVTVFHVAQQTGTPWDIGTVHYVEIPPEGIFDVLECVSLTYTVDAKSTLETKLELAPPPSQGISGGAASGVSGLLSSANNLLSDLTTKGIARRVQAGVQIIGGQYPSSWTSAALSAIANPINAITSVVNSLLAKEDEKPPKQPPMRLPPE

Entity 2 polymer

描述 description	Tail-tube, gp21
分子量 formula_weight	14673.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E1,a1,f1,g1

MACNKQNGVKNILITFTDCDTQEVIGPISHEQPDDTLPTYKNCAWTNTALTNGYVQRSASNATMTLPVVRDLRVPLAFYQGCAQVDVQVEKFDGTVMTLTEGAVVEPEESDGRSVTMNIVASEIDELLPPGSLAAA

Entity 3 polymer

描述 description	Baseplate Wedge 2 protein, gp29
分子量 formula_weight	43322.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	F1,G1,h1,i1

MSCTIQRPDPQDLRNDIATRFSTNVLGGAPIIPESNEFYVVSLEYAMQEEFYAFGEQMWRERDPRFACCENLVKMAAERGVYPKPAQFAQGYVRMTGTPGSALNQGLRFQFGNQTYEPASVVPDQLPATGILVLRVSAVNPGPSGNARVTDGTLVTPVPGISSAVTAYGGNFCGGSDEEECEQFRTRYLQRLQYQPRFTVEWLKSKAAEWPCVTDVFDLGPNCCAVNALGEVVCPNNFEFYVLFRDTFDCGLAPQCVVDEITDWLFGSPQGLGLGEAEFGICGKVRTAAPVKLDIILDGLSCATPAQSRVVEERVTDFVNRLPPSTNLTIDQLRFIGLQVLGPSFNFNVAIRSPNDAVQPGLRFTSCGDAEIDCDYKACLNSVVVINNNVTTSGCL

Entity 4 polymer

描述 description	Baseplate wedge 1, gp28
分子量 formula_weight	19318.7 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	H1,j1

MTCTVDVADRRKRFWTTQIAACGTSSDDCGDCARPGLQLMCNGQGQVTVSTDNYAVGLALNILLTDASKADTGCGWTPGNRGGFWGDSFRSDNLRSGSKIRQVPTRTSMRETVSLIRAYALDDLKKLVTYGVAKSVDVDLTYRGSNKIDMTVIIQGVDGNESRVGLTGERISNAWVWS

Entity 5 polymer

描述 description	Tail sheath protein, gp20
分子量 formula_weight	53896.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	I1,K1,k1,m1

MAQDALSDGFVRLCIDPSLNFFGEGCKILVEGQMTDDGSATPDAVTCVTSELDIIERFGQGSVLTESLRKVFCTCKSGVSVYALPREDAAAGVKAVYTLTIAGPATTDGRVQLYMGEAEYAVDIGVDAGDTATDIAAAIVAAISPDFPYAATAAAGVITLTARNAGTIGNHLSVIYTNLGSCTSVTPEGVTVTFAQTTAGSVNPTPNDYATVVNECCFAVYVLSSDDTDWQENLRDWIRSAWDCSKPQCFGHGYVFNKGTLGQVLADGDNSAELSRLALPTTYPVLPYLTNAAYGALSACSTCNNPELNIQGQTFGLLSCINMPESCTPGWTFGEVTQLQANGFVVSGPSTTSGQGNYTSPYIYNDVTNYLRDEKNRPNATFRDASSRRLAAATGVALAEFLQQFNGLAVFTKNTNIRTGIIGTNPRLMLGKIRKWAQDNVGTLFSEFDNINEDIQLLTDFEVQPKCVGQPGIFHLNMRYRPPVRGARINVNMAPALFDNCDR

Entity 6 polymer

描述 description	Baseplate Wedge 3 protein, gp30
分子量 formula_weight	31414.9 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	J1,l1

MNVLIPGIDGMVSAGTLEYTGCCPPSFADVDECTLATAFVGLLPSGPLWDRPKYEAITTITEAGNCAACWTTDHCPTLVDYAVNVGARLASVIERTIWPAVRESDPFTAVTSTADWLNRFDWVNCFETSCRSKELGEKTPIEYMTDCGPVYVKITYPPSLQQAFESALIKSLERLSMGIIKNLAAINFVIEPLKVRVVPVDTTDACENETLCVVLEKTSDFFDGVNANTCGIPTPVAAYIDRDVMQLPSDLDKYIWPGHMAAECIVRSLLSHVSRFCLIRTEQAPD

Entity 7 polymer

描述 description	Tail Spike protein, gp124
分子量 formula_weight	61649.8 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	P1,Q1,R1,r1,s1,t1

MAKLRPLQVGGVPGCANIPGGEDCQCWPEWTADNGYFFGDVVQQGGVLYYATRDVPPGTPFLAADWAPYRPAATAIPPHNENSTYFQYQPVAYNDKLYTARTDLPPGPFDPANWQEISVEGLVEVVDSATIDFTGTGAAGDPVSADVKLDPDPDNLLSATANGLILTADNIPFPDPSQILISEEVTLRVDYVTGDDATADGTLAKPFATVSAAIGVATTGDRVEIYPGTYIGNFAPKSDVTVVGLEGVVIDGDVTIAAGVSGALVDGLFVDGSVLVNGANGSVTFRNSRVTENVLATGNNTGVYRFENCDIETAAIVNGTGNAEFIFSGGVSENDFFLNSPGTMIVENRSRVKAVLHEAGNMIVQNIGVIESLASTPDNGFLAVMSSSLFDPLTSTYGTISKTGLCPFVFQDFGRDNTDTTALNGPKFIVSNGRDVHGNYDPAFYALPNGQTLNSHFAGIDAALETLQEYSPLDRLVPVDLGFSFTGGWTDGETIGAHVVSRSTIVPENMAGSVFSTDSSTLDGVLNIVVGPSVVGTVTIVDGIATFASSSFNLDPGQTVRVVTTSDGTFDYAALTLVGHREVVYVN

Entity 8 polymer

描述 description	Short Tail Fibers, gp31
分子量 formula_weight	31667.6 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	S1,T1,V1,W1,X1,Y1,v1,w1,x1,y1,u1,z1

MAGIFFSGGLACNLTVNAACGIATTGDDCPALYYPPKCNVQVDPLQMNAVISEIANAINAFGNTYDCSRLDNLKQVLNRARNICDLPPFGDAPDMDDRIAGCFDGQSSTVTVQQLVNLVLGQVGTLCQLPQIGAIQDDDWLAGCIDGAARIVPFAAVRSALGGGGGVIGGVIPQNQLFDSWRAGGFWDVSQSTAGRTAFVFRSRKEGIGITVSELFIATGGGAYQSISEWEPSTFAYVPTGETTAIDGGRIQAVAIAFKKGNQWYAKAGDIILPLGGDDGVIRVRTPGYQRLQIWDGVQV

Entity 9 polymer

描述 description	Baseplate Centerpiece, gp25
分子量 formula_weight	43287.0 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	U1,e1

MAGPCYNPDAEYLPASFKGFSFDADSSDSDHGRNGAEAEFVFGERTGYADLGIKIKSYQLRARFQTNDHIAQTNAFIAVLESPGPGLLVHPTRGTVFAACRSARVTDSKVDAAGVTYVELDFVEANSVLSGFGLVGNLVALALAPIITATEGSFKRHFSPDNIRYYNTEAVVSTMAQAVTQVQNAYLAISGNDTSQDKWTTVRDFRNVLIDEFTFYSPANAWNVLRNGFAILDAAATGSDKFNVLRNLINWSSTHSDLDGESGDAENAIFTAVRVLSAAYLAKAYTETAATTVNEGLTQYDLIAAVLEQEAQIAKDDCHDNEFFLQIRAFAVDVARVMVNRAYNSPSLIVYAFPGTVHGLVAAWEIFGDAKRSRDLEARNNGSPWAVGPKIISERVRA

Entity 10 polymer

描述 description	Baseplate Central Spike, gp27
分子量 formula_weight	20720.5 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	A

MTTSKTYDERNRDIQDGFERHVFKGIEHTDTGALVSVKGSGTQEEDVPVINSGYGFTPAADTELEVFLHGDGSDASNKFATMTIPRNKQRKWPEGAGGVQHPFNADKFVQFDDDSIWLKDGKFTLGNNQELTITVSNGLVTLSSNNEVDFRCPKLMHNGVNIGDSHVHPQKPDSGGDSEEDTDPPKRD

Entity 11 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (1)

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分辨率 resolution	3.20 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	14856

fit	/app/data/saxs_computation/fq/8fqc/8fqc.fit
pddf	/app/data/pr_computation/fq/8fqc/8fqc.pr.out
profile	/app/data/saxs_computation/fq/8fqc/8fqc.dat

Structure of baseplate with receptor binding complex of Agrobacterium phage Milano

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

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 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)