SAXSdb — 9ngy

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9ngy
沉积日期 deposition_date	2025-02-22
结构标题 title	In situ cryo-EM structure of protochannel (DotA-IcmX) of the Legionella Dot/Icm T4SS machine
关键词 keywords	Type IVB Dot/Icm Secretion Machine, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	67.85 Å
回转半径 Rg (电子) rg_electron	68.08 Å
零角强度 I(0) i0	6781470000.00
分子量 molecular_weight	718570.0 kDa
排除体积 excluded_volume	907500 Å³
包络体积 envelope_volume	1270700 Å³
水化壳体积 shell_volume	161290 Å³
包络直径 envelope_diameter	282.5 Å
壳层 Rg shell_rg	66.39 Å
包络 Rg envelope_rg	67.90 Å
形状 Rg shape_rg	68.07 Å
总 Rg total_rg	68.09 Å
总原子数 total_atoms	50535
残基数 n_residues	6585
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	225.4 Å
Rg (实空间) rg_real	67.24 Å
Rg 误差 (实空间) rg_real_error	1.70 Å
I(0) (实空间) i0_real	6.7470e+09
I(0) 误差 (实空间) i0_real_error	1.4280e+08
Rg (倒空间) rg_reciprocal	66.40 Å
I(0) (倒空间) i0_reciprocal	6759000000.0000
解质量估计 total_estimate	0.8118
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	68.6 Å
偏度 Skewness skewness	0.664
峰度 Kurtosis kurtosis	0.100
角度范围 angular_range	— – 0.1150 Å⁻¹
当前正则化参数 α current_alpha	0.0265
最高正则化参数 α highest_alpha	984300000.0000
实空间数据点数 n_real_points	24
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.719; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.385

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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 (3)

Entity 1 polymer

描述 description	IcmX (IcmY)
分子量 formula_weight	50712.4 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	AP1,BP1,CP1,DP1,EP1
原子数 atom_count	50535

MKVLPKLALANLVCFTTLSVFAQPADPSGQQTSTNTSNLVTYLTNLGKYLGYDITQSSKAPNPPYSQLFNSNVVQLVQNYAYNTFLGAIPVDAMSQSLMNFVTDKVQGNSLINNLANTTFKYQNFSAPSSGADGKITANGLIDQSTASAQTPTTPGIFSAPQITTSGTYLNDPVSQAVFNILGTPDYSFCMDNEQKNWLPNCNLMYQNLVMQNVIGTLPPAQTSGSTPAFYSYKYNQPLISQLNSNSLIAPLLMDTSASQSGQDSGLTAKSQAQQALNFIRYASAQVTPPSLPKLSAYSELWNQATAKPNSAGYNEVQQKQAAATLSSYFNNLRVYAAQTSVGVSNLYYILSKRLPQNMSADQSNANITSQALNEFNMATRRLFDPTASNTPGQPNQQWIKQINDASPATVQKEIAILLAEINYQMYLDRQIQERILLTNSIMLLQNLKAAQPTADFSSQGSPSEQ

Entity 2 polymer

描述 description	DotA
分子量 formula_weight	113235.6 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	FP1,GP1,HP1,IP1,JP1

MNKLAITVLLCFFPALALAENGALSFAPPASDLSVVFLGNLFGVVDGVLHGTGSQIMGNMFGVFNSAVLALGGIIIMYTLMVSTMNTAHEGQMLGQKWSSIWIPLRSTFGLALLIPKASGYCMMQVFFMWVIVQGVGAADKIWEAALSYLNRGGVIIQAQADPTKSLQAAGSSSSGVAKGALTILGGQICMLGLQKQLQAQRDLYLSQSKSPPCGGNPTPEMNTFCRTAIPDFISTVNFVKKQNDDTPKDLTANQPASFELDMPNFDKSSPFYFLNGICGTVKWNNISALNSTNQSDNKGLVTVGGAGSNSSMGANSLNITSSQLQTARLSRAIAIQQMYVTLSTVAQVMVNNDPAFSTTTSTGNSKNDFSAIAKQQFGVPYKSSGEVCTEYQQVCQTWGSVPSSTGSTTGVLFNGTEFLGAINDYNGIMMPTLNLIRQATSKEFDKKSRDFIAEANAKGWIMAGSYFFDLVKLNGSATEFADQFDTGTGLDKSSFDPTQLTKPFGKTCQDPYSLLCTWFQNKSDKLIQIQSLIDGVPALGQDGVKQPDLSDNPQRQSVSGPLSSTVYGFVNNSMMVQLPGQPGIKPLTFANLINFKVDTSLYYMKHQDFDCGRVKILFFSFCLGRMMGDLFYNYVFRYVYNFFLAIFGEMINSIVMAFLMIPLQGMKDIFIVGVQTLTQPGINPIVALANMGTMYINFSGTLWLTLLNMAVVSSLIPLFGIFIFALIMMAMPLLMAWIGTMVSIGFVTAYYIPVLPYMIFTFGSFAWLIAVIEAMVAAPIVALGVTHPEGNEAFGKGEFAIMILVNVFLRPSLMIIGYIAAIALSYVGVWILNAGFDHAISYIQSDQGIETWEKGTSSNDAKRFFQSAGNWTGAKMDTSQWDNFKDKLTGDYQSTALEGGYTGWAGVYAFFFSILIYTSMYLIIVQKAFTLIAHLPDKVLRWIGGSPESFGQETMQWGEEAKGRVEKAGEATYGAEKAIGDKLGAKGQEMLGKLGPQAKKISENAGDVSGKGKNSGGSQTGPSSKPDTGQQLGGSDSGTPTSTPPPE

Entity 3 polymer

描述 description	IcmE (DotG)
分子量 formula_weight	107911.9 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	KP1,LP1,MP1,NP1,OP1

MASKKENLKSLFSNTRTRVIIIFTAALLIIAVVIGFFKIRGATTGSIAAAEVSTVPGGIQSIPGVLDPTAQYAKLQEEQNITQAQVAEKTGGSAIPTIIRTQALGEGVGVIGSQSGVGFAALAQEELGGPQRSLWIQELQDGSCSKSVITKVVNQGAQLTDLKAACSCVQLKDSGYGLQELEQVCECKELKSAGYNARQLKEAGYSAGRLRNCGFDACELRNAGFTAQEMKDGGFSDGELKGAGFSDAEIAKASGLPDGITADDVRKAGCGAAALAKLRQAGVSASAIRKISGCTAEQLKAAGYTAKELKDAGFSAADLRRAGFSAAELKDAGFTARDLLNAGFTPADLAKAGFSDAQIKAAQAELPPGITPQDVKNAGCDVEALKKEREAGVSAALIRQYAGCSAQALKAAGFTDADLANAGFTPAQISAATPLSDAEIKAAGCDPDKLKKLFSAGVSAKRIKELNGCSAEALKAAGYDAQSLLAAGFTPQELLAAGFTPKQLEDAGLNPVSIIADGRVADCSVESLKKARAAGVSALTIKQTLGCSAAALKAAGYTAKELKDAGFTAAELKAAGFSAKELKDAGFTAKELRDAGFSAQELKDVGFSAKDLKDAGFSAAELKAAGFTAAQLKAAGFSAKDLKDAGFSAAELKAAGFSAKELKDAGFSASDLKNAGFSAKELKDAGFSASDLKSAGFSASELKNAGYSADELKKAGYTSAELRNAGFSPQESAVAGLQGPDLQQLDSSITGIPSIPGATPRPTTSDAASSAEQLQAILQKQNEQLAEQKYQQEIQQRTSDMLTAATQLVQDWKQVETQVYTEGTEETKTSGGESAVPGTGTGTGSNNQPVDQGAVSAQNQAIIKTGDIMFAVLDTSVNSDEPGPILATIVTGKLKGSKLIGSFNLPSNADKMVITFNTMSIPGAEKTISISAYAIDPNTARTALASRTNHHYLMRYGSLFASSFLQGFGNAFQSANTTITIGGTGGGNNITVANGVGRSTLENAVIGLATVGKAWSQQAQQLFNTPTTVEVYSGTGLGILFTQDVTTI

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7. 引用文献 (2)

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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	3.63 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	37503

fit	/app/data/saxs_computation/ng/9ngy/9ngy.fit
pddf	/app/data/pr_computation/ng/9ngy/9ngy.pr.out
profile	/app/data/saxs_computation/ng/9ngy/9ngy.dat

In situ cryo-EM structure of protochannel (DotA-IcmX) of the Legionella Dot/Icm T4SS machine

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 (3)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)