SAXSdb — 9hmf

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9hmf
沉积日期 deposition_date	2024-12-09
结构标题 title	Periplasmic scaffold of the Campylobacter jejuni flagellar motor (alpha carbon trace)
关键词 keywords	molecular machines, flagellar motor, molecular evolution, in situ, scaffold, MOTOR PROTEIN, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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	89.38 Å
回转半径 Rg (电子) rg_electron	89.98 Å
零角强度 I(0) i0	3158410000.00
分子量 molecular_weight	491370.0 kDa
排除体积 excluded_volume	602820 Å³
包络体积 envelope_volume	925830 Å³
水化壳体积 shell_volume	95129 Å³
包络直径 envelope_diameter	289.1 Å
壳层 Rg shell_rg	76.51 Å
包络 Rg envelope_rg	83.40 Å
形状 Rg shape_rg	90.20 Å
总 Rg total_rg	89.84 Å
总原子数 total_atoms	1
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	232.5 Å
Rg (实空间) rg_real	85.55 Å
Rg 误差 (实空间) rg_real_error	0.90 Å
I(0) (实空间) i0_real	3.0460e+09
I(0) 误差 (实空间) i0_real_error	5.7290e+07
Rg (倒空间) rg_reciprocal	87.24 Å
I(0) (倒空间) i0_reciprocal	3137000000.0000
解质量估计 total_estimate	0.9205
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	109.4 Å
偏度 Skewness skewness	0.210
峰度 Kurtosis kurtosis	-0.634
角度范围 angular_range	— – 0.0850 Å⁻¹
当前正则化参数 α current_alpha	0.3404
最高正则化参数 α highest_alpha	90230000.0000
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: 0.001; Oscil: 0.992; Stabil: 0.969; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.116

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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	Flagellar protein FliL
分子量 formula_weight	19902.9 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	O,P,Q,R
原子数 atom_count	4298

MDEELENEETKKKKGGSLVIIIVILLFVLLLSIMGVIAWLISSSSSDESEVKEAPKEEAKADKPKVSAPTQRGSDFANIGPMYPLDPFTLNLLSDSGSRYVKCTIELEQNSELLKPELDKKVPVIRDIIIRTLTAKTFEEVSTQKGKERLKDELVGKINEILTDGFIKNVYFTDFVVS

Entity 2 polymer

描述 description	Paralyzed flagella protein PflA
分子量 formula_weight	91084.1 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	K

MRILFLILLSFLNAFAFELVLNTGRENNQAFAVLHASNDLEFTCQKFITEAKVHFECDIVGMVDNKLKDQSFSAFDLKFIQEAQKIKMIILPKIQARMFDTSQNIYIDKELSSSSSHKSKAFTFIFTPELAPIKDYDGLDFNINFPHESLPYVGALDLNSDPVVIPQSADINTYLRIKKEYDKANYNQVVIDAQNAINRYRGSIFTSEFILYKLRAQNKLYTQDPSMRDQQILEKMIDDAKNWTRTFTSDKNFSEVLHIMLRTYIALAQRADVEYTMSILDNEQPNNYFTQLSKLDYADYIYNLNEKEKAVNIYENTYFNTKNLDLAARAAMSLAKNLLSNEQVNKAIEYINTILKANPEYFGKDIPRSLELAKLFNQKGQFDISASIYEDAFAKMSKLDPSYEETLKDLALVLSHANRSSDAKKYLDLYMDDYLDGKYLDEIKKASDEVFFALGDNNASFLHQRYTDLMKQYANKDENIANKALDEDVALYYKEGNFSAILAYKDLIESKKIPNATQFLEKAAINDLKNAIKADNCINAANIFMRFSAYDIGQKIENKKQMLACLIRTSNVEQALDYIDKNYNEDSIFYGLQKASILFDNKQYPQVIKISKDIANSRILKSDDENFKAYYLQFLSLLRLNDYNQAIKILQILESFPMNFSMVEAYDALLSYANDHNMQTTILTYAPKAIDYQNFKGINLFSPNLEFIYLDALTKINKNEESLAVLTDLLKLKLSDEDRARALYIQALTYERMQNIQAEKESLKQCLEIKSASNWQNLCKSKNQILNQ

Entity 3 polymer

描述 description	TPR domain protein
分子量 formula_weight	93534.6 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

MAEQEDIILEKPEDGLNQPRLDESLEGFKGQEGQAPEDEEFASLPEELPQENSESGFKFTRESAPEDVSTFEEVESQEPTPWYKDRKFMSLVGLSLGIICILVFTLFYLTFSEGKIKPDIIASKPLEQPVVMPDESYKYNDMQRIDGMIQKANALYLKGEVEQALKVYEQVAVYNESLSNYNLGVSQMNENKFQEAFESFKKAIANGENQSVAAINAAVCALKLNDKEKFRYYIDLAQVYLPKEGKSKLYDYYLSLINYYKGYYPEALQMLQRTDMEPYSDVAKYLSAKIYAKMDFDSKAIQQLNSQGNFESSLSLGLLYARIGEYAKAKVALSTAMKIERDFNQSLAALTLVDIKTGNYQDMLARLQNSYDNDKDRYKILDAYKIQVRLNKDLFNIAVAQNSFSKDLLKKQKDQFDLLFYFAPYQVFDSKQAALYIKKANVTDFVDDSADAGVYLNTSKALSSTNVKIANIINYALNQKLRLANQEFQKLIKDYPEHSILHYNLALTYAQMQNYELAYKHFSSSYHLNPKNYLAGAFAMFCAKLIDIDTTKLYNEILDNIAADSNFKANMQKSMLFLVNNNYISMLPYLDETKKDTPLSLIFEAIVAKNNNLNNQVDVKIAKLRSELPEDILANILYFNSLNSNLNIKEYAQNAQIHFKNLKLDYRSVFGGPNIAREFYVNLMHIAGLLNLERQKIKELINVSGAKDEGILQTLAYLDIFAQQYEEAYALYNSLIDDYGAKDTKTLFLAAVAAIGANNPNSAIALLQLSKLTDKNNKESKAALGMLYQEVKNYEAAISQYKTLPNNFKSEFFTFDINNN

Entity 4 polymer

描述 description	PDZ domain-containing protein
分子量 formula_weight	41455.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	7

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D,E,F,G,H,I,J

MKKILIICMLFTLSFGIERPKFEDFLAGYERNKASMLNYEGMPAFALSENLLAVLKQPNTKLNKYVKYDPFLNLYLVRTDFSLIPTPMGDEEKLTRNDWVGIWDPNKPYIGHIKYLAQNIDEKDQLDFNSKIGLLGTPCCEMMGIALNNSSFIGNRYLKHFMKYNDVYWGDIGVDFVVRENKIYVNNVRKNPQFLINDQVISVDGLPANDLRKLNEKILFADRGSTLYFQVLRDNMDLNISTEVFAKDLSKFNLPDSKPKPKITNFTSNLGLTVNTSLVVTKIDPKSKASNAGFMVGDKILRVNNIILNNFKELQNILSAGNDFSILIERKSTKLPLSNFNNELGGNANSGGDGKFQFFIRLTK

Entity 5 polymer

描述 description	Lipoprotein, putative
分子量 formula_weight	18545.2 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	C,B,A

MKKIYFMLAIAGIFAGCVPSANSATKNSSANSTAPSQDVIVQKVDKDDVRDIIREEKMLAPDASETELSFTAVGEGIAPMNTVSTAQALALAKRAAITDAYRQLASKLYGVKVNGKDTVKDAMLRSSTITAQVNGLIKNASIIDENFNQGLYRVNLELKIDADKWKELFAY

Entity 6 polymer

描述 description	Chemotaxis protein MotB, putative
分子量 formula_weight	27817.7 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	M,N

MAKKHKCPECPAGEKWAVPYADFLSLLLALFIALWAISKTNPAKVEALKTEFVKIFDYTSTQTVKEESKTQEKYKGAAKEESDELKSLKQMTMTQQETIKRLQAALDQSDNQVALNLPSKVEFERGSAQIVSADIQDYLKRMAELTTYLPPQAKIEIRGYTDNSDSIIRSYELAYQRAENVLKYFIEGGANLKNISIKSYGLNNPINGNPQALENNRVEIYFKVDTADTSTQKSVLELINKIGTKAP

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7. 引用文献 (2)

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分辨率 resolution	7.90 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	32790

fit	/app/data/saxs_computation/hm/9hmf/9hmf.fit
pddf	/app/data/pr_computation/hm/9hmf/9hmf.pr.out
profile	/app/data/saxs_computation/hm/9hmf/9hmf.dat

Periplasmic scaffold of the Campylobacter jejuni flagellar motor (alpha carbon trace)

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 (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

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)