8qja

T6SS-linked Rhs repeat protein - Advenella mimigardefordensis VgrG-Rhs core

Method: X-RAY DIFFRACTION D_max: 229.2 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8qja
沉积日期 deposition_date	2023-09-13
结构标题 title	T6SS-linked Rhs repeat protein - Advenella mimigardefordensis VgrG-Rhs core
关键词 keywords	Rhs, T6SS, VgrG-Rhs, toxin cannister, Rhs-repeat, CELL INVASION; CELL INVASION
实验方法 method	X-RAY DIFFRACTION

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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	75.81 Å
回转半径 Rg (电子) rg_electron	76.75 Å
零角强度 I(0) i0	3401590000.00
分子量 molecular_weight	472760.0 kDa
排除体积 excluded_volume	582650 Å³
包络体积 envelope_volume	955600 Å³
水化壳体积 shell_volume	113650 Å³
包络直径 envelope_diameter	267.4 Å
壳层 Rg shell_rg	62.72 Å
包络 Rg envelope_rg	75.41 Å
形状 Rg shape_rg	76.74 Å
总 Rg total_rg	76.55 Å
总原子数 total_atoms	33470
残基数 n_residues	4088
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	229.2 Å
Rg (实空间) rg_real	75.87 Å
Rg 误差 (实空间) rg_real_error	1.51 Å
I(0) (实空间) i0_real	3.3880e+09
I(0) 误差 (实空间) i0_real_error	6.8680e+07
Rg (倒空间) rg_reciprocal	72.93 Å
I(0) (倒空间) i0_reciprocal	3376000000.0000
解质量估计 total_estimate	0.8123
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	54.6 Å
偏度 Skewness skewness	0.557
峰度 Kurtosis kurtosis	-0.513
角度范围 angular_range	— – 0.1050 Å⁻¹
当前正则化参数 α current_alpha	0.0280
最高正则化参数 α highest_alpha	284600000.0000
实空间数据点数 n_real_points	22
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.793; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.207

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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 (1)

Entity 1 polymer

描述 description	Putative type VI secretion system YD repeat-containing Rhs element Vgr protein
分子量 formula_weight	212823.0 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	33470

GSGSMNRTVNATTPLGDKLKFKSLKGHEQLSDLFEWTVEFVSDSPGLVLEDLLGKTISLEVETSAAPRYMHGVITAFKLVHRETQTRRYYIYEATVRPWLWYSTQVTDNRIFQDQTAVQIITQVLQAYDYPIENRLVGQYRKWGYSVQFQESDFNFISRLMEHEGIYYWFRHEKDQHVLVLMDDAHSHAPLPVMPDIPFYPDDTRSVPLEEYIRDWQIAGELTPTTYSTMDYDFQKPQAEMSARRWVKNQNTQGLDLDWYDPMGGYVDSADSDHYARVHLESMQCLQEQAWAVSNVRNLAPGYTFSLKYYPNSEENKSYLILRAEYDFRDPSYASAGGVQENATFVIRSQHIPASVQFRAPRSTPAPRMSGPQTATVVGPDGQEIWTDKYGRIKVQFHWDRQGAMDENSSCWLRVSSPWAGGGFGGVQIPRVREEVVVDFINGDVDRPIAVGRVYNASNMPPVSLPENATQSGFLTRTKNGTPENANKMLFEDSQGNELLSMVAEKDMNTHVKNNQQHDVVGNAVSSIGGLRSHTAHSTSSITMASGAVKSYQSNHNRTVQASLDDSVGGNLEQTLSDGVDETITGAHSHTVSGAASHQLLGLHVNTTTQDVETVNGTVTETVSADETTNVTSSSELEAADITLETPSLYKESTKQDININAGGSLDIQSTGPGIIQTPTDIEKESPANLEAAVMLDNNTVNREDKYILKLNLDAMSDVMVSGAKTDRNIADLAFYGMGGTMQLANVGIYGASIQMGSSDQKMGLASLSITGLELDKGFKIKTMGAGGRSGYKGKHRAAGGGRGPRGGKGGRHRAGNKGDPKKPHADCKECRGRVGGSIGLDVGDERFSHLDFVLPGVFPLEWNRTYRSNMTAKDGQGELGPRWITAFTLVVLPLETGGYEYISEVGRAVSVIELEPGQEWYDRTEELIWRRPDVDTLEVSQKYQRTETFERSGDVFRLKTIADRAGNQAQLIYDAENGFLVRVETAIQTVHLDHDAHGRITTIWHEVTGDDGTPLRRTLARYQYDEAHDLVAAVDQYERTHTYAYQNHLITRYSDKTGRGINLEWDGDHPQAKCVREYRDDGSNLLRFRWDESESKTYVTDALSATTVYTFDAHNYIIHIDFADGTRQSRIRDEFHNIVEVRYPDDSFEKYEYDEFDNILKLTRADHTTVGWEYDQYSQITKIVDPGGNIWTRDYDQFGNMIRETDPKGHTSEFQYTAEGLLIQSVNPAGGVSTLSYNPAGLLIRYSDCSNKTRRWEYDLLGRTVKQTDPCGNAESYEYNRYGFINEVRRPDGSVLTLDFDEEGRLLSFIDPIDNLTVYAYDGAGRLARKTDPLKQDFHYNYDKKGRLASLQDENGAQFTFQFDPVDRLIRTVGFDGKVKKYNYDKPTGLLFSMEDADRETHFEYDVMGQLLKRRAGHLVDSFEYDISNRIIRAHNEYCDQHFEYDVLNNPIRETHIYNAFGQNREYVWENEFDELSNRLTTRRPSGEKVSWLRYGAGHVHGILLDDQEVLSFERDNSHRAVRKRQSNSLLAVTNYDVMGRVKEQKLNLAQGNRTNLRSRQYAYGLDGSLVAIEDSRHGTTTYRYDALDRLVSATAFNETELFAFDPASNLVDRDKTERSKPANTFPKNVSKVLGNILKRCAGMHFEYDAQGNLIRKRKPDSLQEFEWDEFGRLRKTVNTDLNSKHVSEAEYIYDTFDRRIGKVNQQETSGAAVTFYGWDGHHLAFEESTVGDAVDKTHYLYEENSFVPLIQYQYSADNTIAEGRNHLSVSHYQCDHIGTPQLLTDDNGHIVWEGRYSALGKQLDSIGGDAGVAGGQNNLCYQGQYYDRESGLHYNRFRYYDPDIGRFIQQDPIGLFGDSNFYTYAPNTANWIDPFGL

来源 Source

来源生物 organism	Advenella mimigardefordensis DPN7
NCBI 分类编号 ncbi_taxonomy_id	1247726
宿主生物 host_organism	Escherichia coli B

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7. 引用文献 (1)

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晶胞边长 a length_a	66.239 Å
晶胞边长 b length_b	97.783 Å
晶胞边长 c length_c	215.006 Å
晶胞夹角 α angle_alpha	85.69 °
晶胞夹角 β angle_beta	89.99 °
晶胞夹角 γ angle_gamma	76.89 °
晶胞分子数 Z z_pdb	4

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	3.360 Å
最低分辨率 resolution_low	48.480 Å
R 因子 r_factor	0.2598
R_work r_work	0.2568
R_free r_free	0.3173

fit	/app/data/saxs_computation/qj/8qja/8qja.fit
pddf	/app/data/pr_computation/qj/8qja/8qja.pr.out
profile	/app/data/saxs_computation/qj/8qja/8qja.dat

T6SS-linked Rhs repeat protein - Advenella mimigardefordensis VgrG-Rhs core

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

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (1)

Entity 1 polymer

聚合体 Polymer

来源 Source

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)