SAXSdb — 8hqz

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8hqz
沉积日期 deposition_date	2022-12-14
结构标题 title	Baseplate of DT57C bacteriophage in the full state
关键词 keywords	Baseplate, T5, VIRUS, 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	71.02 Å
回转半径 Rg (电子) rg_electron	72.09 Å
零角强度 I(0) i0	1393880000.00
分子量 molecular_weight	313630.0 kDa
排除体积 excluded_volume	392330 Å³
包络体积 envelope_volume	659510 Å³
水化壳体积 shell_volume	86882 Å³
包络直径 envelope_diameter	281.5 Å
壳层 Rg shell_rg	59.20 Å
包络 Rg envelope_rg	70.47 Å
形状 Rg shape_rg	72.11 Å
总 Rg total_rg	71.71 Å
总原子数 total_atoms	22127
残基数 n_residues	2830
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	220.2 Å
Rg (实空间) rg_real	68.69 Å
Rg 误差 (实空间) rg_real_error	1.71 Å
I(0) (实空间) i0_real	1.3740e+09
I(0) 误差 (实空间) i0_real_error	3.1530e+07
Rg (倒空间) rg_reciprocal	67.86 Å
I(0) (倒空间) i0_reciprocal	1383000000.0000
解质量估计 total_estimate	0.8286
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	60.1 Å
偏度 Skewness skewness	0.575
峰度 Kurtosis kurtosis	-0.349
角度范围 angular_range	— – 0.1100 Å⁻¹
当前正则化参数 α current_alpha	0.0708
最高正则化参数 α highest_alpha	67010000.0000
实空间数据点数 n_real_points	23
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 0.992; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.234

▶

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

▶

5. 实体与聚合体信息 (7)

Entity 1 polymer

描述 description	Baseplate hub protein
分子量 formula_weight	107114.1 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	A
原子数 atom_count	22127

MKQILDSARNYLKNNSRIKTASLISLELPGSTGTSTAFIYLTDYFRDVIYNGILYQAGKVKSISPHKQNRDLSIGSLSFTITGTAQDEVLKLVQNGVSFLDRTVSIHQAIITEDGSILPVDPDTNGPLLYFRGRITGGGIKDNISTSGVGTSTITWNCSNQFYDFDRVNGRYTDDASHRGLEVVAGQLLPSNGAKRLEYQEDYGFFHANKSISILAKYQVQEERYKLKSKKKLFGLSRSYSLKKYYETVTKEVDIDFNLAAKYIPVVYGVQKIPGIPIFADTELHNPNIVYVVYAFAEGEIDGFLDFSFGDNPMICVDANDSSARTCFGTKKIVGDTMQRIASGISSSSPSVHGQEYRYNDGNGDIRIWTYHGKSNQTASDVLVNIARNRGFYLQNMNGNGPEYWDARYKLLDTAYAVVRFTINENRTEIPEVSAEIQGKKVKVYHSDGRVTANSTSLNGIWQTLDYLTSDRYGANITIDQFPLQQLIQEAAILDIIDESYQVSWQPYWRYVGWTNPLAENRQIVQMNTILDTSESVFKNVQGLLESYGGAINNLSGQYRVTVEKYSNTPLEINFLDTYGDLELSDTTGRNKFNSVQASIVDPALSWKTNSITFYNSNYKEQDKNLDKKLQLSFANITNYYTARSFADRELKKSRYSRTLSFSLPYQFIGIEPNDAIAFTYDRYGWDRKYFLVDEVENSREGKINVTLQEYGEDVFINSGQVDNSGNDIPDISNNVLPPRDFKYTPTPGGLVGSIGKNGELSWLPSLTNNVVYYSIVHSGHAEPYIVQQLETNPNERMIQEIIGEPAGLAIFEIRAVDINGRRSSPVTLSIELNSAKNLSVVSNFRVTNTASGDVTEFVGPDVKLAWDRIPEEDIIESIFYTLEIHDPQNRMLRSVRIENQYTYDYLLTYNKADFALQNSDALGINRKLYFRIRAEGDDGEQSVEWASI

Entity 2 polymer

描述 description	Distal tail protein
分子量 formula_weight	22666.5 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	H,I

MRLPDPYTNPELSGLGFESVNLIDNDPVIRDELPNGKVNEVKVSAQYWGINISYPELFPDEYSVLDAFILEYKRTGGYIDVILPQYEAFRVRGNTNLVNIPAGQKGSNITMDTQGVLTGIPKPGDLFKLSNHPKVYKITSFNRSGNSWSINVYPDLFITTTGAEKPVFNGILFRTKLMNGDAFGSTLNNNGTYSGISLNLRESL

Entity 3 polymer

描述 description	Minor tail protein
分子量 formula_weight	34513.7 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	L

MYYSLMRESKVIVEYDGRAFHFDALSNYDVQTSYEEFKTLRRTIHRRTNYADSVINAQTPSSISLAINFSNTLTEANFFEWLGFDRKGNTFLLPLYSNNIEPIMFNIYIVNKDNNCVYFENCYVSTVDFSLDKNIPILNVGIESGKFSEVSTYREAASIIQGEAMSYSPVIVSTNGNILPGLISASLSFQQQCSWREDKSVFDINKIYNNKRAYVNEMNASATISLYYLKRFAGDMVYNIEPETDVPLNIRNNNISIDFPLARISKRLNFSDVYKVEWDIIPTASSDPVRIDFFGEIKND

Entity 4 polymer

描述 description	L-shaped tail fiber assembly
分子量 formula_weight	15384.2 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	Q,R,S,T

MSTENRVIDIVVDEKVPYGLIMQFMDVDDSVYPPSEIPVNLTGYSLRGTIKSSLDENAETLASFTTSIIDAAQGAAAISLSVADVTNIGEKASKERDKYNPRQRFAGYYDILMTRDVIGSEVSSFRIMEGKVYISDGVTQ

Entity 5 polymer

描述 description	L-shaped tail fiber assembly
分子量 formula_weight	113712.5 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	d,e,f

MALKTKIIVQQILNIDDTTTTASKYPKYTVVLGNSISSITAGELTAAVEASAGSAAAAKGSEIAAKESELNAKDSENEAAISAGASEESASQSAASAAESERQAGLSKGSADNSAASAQESEGFRDSAELAAQNAEQSRLLAEQAKTAAQQAQTAAEAAKTGAETAKDGADAAATTAGEHAAAARQSELNAKISETNAAGSATEAGDKAIDATTEADRAKAEADRATQIVDSKLDKVDISGFIKVYKTKAEADADVVNRVLDEKVLVWNQTNSKYGWYKVAGTAETPVLELVETEQKLTSVNNVRADDAGNVQITLPGGNPSLWLGEVTWFPYDKDSGVGYPGVLPADGREVLRVDYPDTWEAIEAGLIPSVSEAEWQAGASLYFSTGDGSTTFRLPDMMQGQAFRAPTKGEEDAGVIKDQIPYVVTVNGISPDAITGNVEIDTSLQGTVSINQGGTGATTKEDARIALELYSTTEVDSALADKADIATTYTKTEVDSALADKADIATTYTKVEVDSALADAKTQSDTDYLLKANNLSDLADRAAAWLNVRPIGSTPLAGDPVGDYDAVTKRWVENKINTGTVGPTMNGVMNYGVGDFHLRDSRAYIQPYEVVSDGQLLNRADWPELWAYAQMLSPISDADWLADPTKRGQYSLGDGSTTFRVPDRNGVQTGSISALFGRGDGGASSTGGTILDSAAPNITGSFGRLVYASTGTIYEANTGTGAFSAVLSQAKYKRLSEISAADGTAATYPSGFEFFASNSSPVYGRGSTEVRPKAFTGVWVIRASGGFVAANTSWSVINGDATRPADGTTADGGEIISRYNVNGVREAQMSWRIRAQIGAEHYARLNVYNATANRTAVYDFNDLGTFSAENLHSKGAIYSDGNLTIQNQGWPGINFKSNRYNTPATQIGGSTIIEVSGTDGNVSGVNLIRRRGDGNQAGQIIVSFPTTGGAIALQGTSGIEYKKDVTDADAQEAMDRINGQRLVNFVYKDDEQERVRFGVIAEEAELIAPQYIKHNQVSYEDILDEEGNKIGEKTRDRPSVDVNPIVMDLMGCVQALNAKIAALEARIAELESKE

Entity 6 polymer

描述 description	Tape measure protein
分子量 formula_weight	132626.4 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	k

MTDKLIRELLIDVKQKGATRTAKSIENVSDALENAAAASELTNEQLGKMPKTLYSIERAADRAAKSLTKMQASRGMAGITKSIDSIGAKLDDLSIAMIEVADKLEAGFDGVSRSVKVMGNDVAAATEKVQDRLYDTNRVLGGTARGFNDTAGAAGRASRAIGNTSGSARGATRDFAAMAKVGGGLPLLYAAIASNIFVLQSAFEQLKLGDQLNRLEEFGVIVGTQTGTPVQSLARSLQEAAGYAISFEEAMRQASSASAYGFDAEQLNKFGLVARRAAAVLGVDMTDALNRVIKGVSKQEIELLDELGVTIRLNDAYADYVKQLNAANTGITYNINSLTTFQKQQAYANAVIAESTKRFGYLDEVLRATPWEQFAANADAALRTIQQAAAKYLGPVIDAINTVFYTSQASISAEAARAQEQTNKQIDPTNVGAVALSLSASEEGYNKALDMYKESLDKRNKLKSEFDKRMEQADFYTKLAIRQVGEGIPAGLATAGASEANKKFVEETAAMGLQVARLDKEVTDSTENLNAWKSAYQAAGAAAAKANPEFQKQINLQRDTTDPGAVYDFNSTVLKGLTEQQKAYNQTKKTASDLANDIQNVAQNTDTAAKTSATLADAIKNIESLSLGTGKSADEYVKNLNLGYNTLSEMKTASQALSEYVKLTGNETKNQLAVQQKIADVYNQTKDKEKAQEAGRRLELQQLEEQEAALRRVLQTNQGNKAVEREIEKIQLEKIKLTNQGMEAQKKVKDYTDKILGVDREIALLNNRTMTDTQYRLAQLNLELTIEKEKYEWYTKQADKQKEAEQSRRAQAQIEREIWKFHQDQQAEMTSKRQEAFENTLTSMFPLAGEMQKMEMQLDFYTQMKELTKDNANEQMRWNAEIAKTRAQMSALTAQRNAQMQSSVGSSLGAVYTPTTGLSGEDKKFADMGNQLASYDQAISKLSELNSEATAVAQSMGNLANAMIQFSQGSLDTTSTIAVGMQTVASMIQYSTSQQVSAIDQAIAAEQKRDGKSEASKAKLKKLEAEKLKIQQDAAKKQIIIQTAVAVMQAATAVPYPFSIPLMIAAGLAGALALAQASSASGMSSIGDSGADTASYLTLGERQKNIDVSMSANAGELSYVRGDKGIGNANSFVPRAEGGNMYPGVSYQMGEHGTEVVTPMVPMKATPNDELKNSSNSTAGRPIILNISAMDAASFREFASSNSGALRDAVELALNENGASLKTLGNS

Entity 7 polymer

描述 description	Tail tube protein
分子量 formula_weight	50759.1 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	p

MSLQLLRNTRIFVSTVKTGHDTTNTQEILVQDDISWGQDSNSTDITVNEAGPRPTRGSKRFNDSLNAAEWSFSTYILPYEDTTTGKQIVPDYMLWHALSSGKAIDLDGDTGAHNNATNFMVNFKDNAYHELAMLHIYILTDNAWSYIDSCQINQAEVNVDIEDIGRVTWSGNGNQLIPLDEQPFDPDALGIDDETYMTIQSSYIKNKLTILKIKDMDSDKEYDIPITGGTFTINNNITYLTPNIMSRVNIPIGSFTGAFELTGSLTAYLNDKSLGSMELYKDLVRTLKVVNRFEIALILGGEYDDERPAAVLVAKQAHVNIPTIETDDVLGTSVEFKAIPTDLDTGDEGYLGFSNKYTKTTVANLIATGDGAETPPILVESITVKSAADATSVTNSDTLQMSVEVTPPEATNTAVTWSISSGDAATIDAESGLLTADVSKTGEVIVKAVAKDGSGVEGTKTITVSAGE

▶

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	—

分辨率 resolution	3.80 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	42697

fit	/app/data/saxs_computation/hq/8hqz/8hqz.fit
pddf	/app/data/pr_computation/hq/8hqz/8hqz.pr.out
profile	/app/data/saxs_computation/hq/8hqz/8hqz.dat

Baseplate of DT57C bacteriophage in the full state

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 (7)

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

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)