9nu3

Uromodulin filament lattice in the kinked arrangement from human urine

Method: ELECTRON MICROSCOPY D_max: 278.2 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	9nu3
沉积日期 deposition_date	2025-03-19
结构标题 title	Uromodulin filament lattice in the kinked arrangement from human urine
关键词 keywords	Kidney, urine, uropathogen, filament, lattice, ANTIMICROBIAL PROTEIN, kidney disease, UTI, urinary tract infection, infection; ANTIMICROBIAL 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	— Å
回转半径 Rg (电子) rg_electron	108.30 Å
零角强度 I(0) i0	6144330000.00
分子量 molecular_weight	633530.0 kDa
排除体积 excluded_volume	777760 Å³
包络体积 envelope_volume	2065200 Å³
水化壳体积 shell_volume	167590 Å³
包络直径 envelope_diameter	329.2 Å
壳层 Rg shell_rg	97.12 Å
包络 Rg envelope_rg	98.36 Å
形状 Rg shape_rg	108.30 Å
总 Rg total_rg	108.20 Å
总原子数 total_atoms	44189
残基数 n_residues	5475
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	278.2 Å
Rg (实空间) rg_real	105.40 Å
Rg 误差 (实空间) rg_real_error	0.73 Å
I(0) (实空间) i0_real	5.8530e+09
I(0) 误差 (实空间) i0_real_error	1.0890e+08
Rg (倒空间) rg_reciprocal	109.70 Å
I(0) (倒空间) i0_reciprocal	6163000000.0000
解质量估计 total_estimate	0.8866
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	139.1 Å
偏度 Skewness skewness	0.046
峰度 Kurtosis kurtosis	-0.498
角度范围 angular_range	— – 0.0700 Å⁻¹
当前正则化参数 α current_alpha	1.5130
最高正则化参数 α highest_alpha	440500000.0000
实空间数据点数 n_real_points	15
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.977; Stabil: 0.942; Sysdev: 1.000; Positv: 1.000; Valcen: 0.779; Smooth: 0.001

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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 (4)

Entity 1 polymer

描述 description	Uromodulin
分子量 formula_weight	69821.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	18

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,A,D,E,J,G,B,N,P,F,K,H,I,O,Q,R,L,M
原子数 atom_count	44189

MGQPSLTWMLMVVVASWFITTAATDTSEARWCSECHSNATCTEDEAVTTCTCQEGFTGDGLTCVDLDECAIPGAHNCSANSSCVNTPGSFSCVCPEGFRLSPGLGCTDVDECAEPGLSHCHALATCVNVVGSYLCVCPAGYRGDGWHCECSPGSCGPGLDCVPEGDALVCADPCQAHRTLDEYWRSTEYGEGYACDTDLRGWYRFVGQGGARMAETCVPVLRCNTAAPMWLNGTHPSSDEGIVSRKACAHWSGHCCLWDASVQVKACAGGYYVYNLTAPPECHLAYCTDPSSVEGTCEECSIDEDCKSNNGRWHCQCKQDFNITDISLLEHRLECGANDMKVSLGKCQLKSLGFDKVFMYLSDSRCSGFNDRDNRDWVSVVTPARDGPCGTVLTRNETHATYSNTLYLADEIIIRDLNIKINFACSYPLDMKVSLKTALQPMVSALNIRVGGTGMFTVRMALFQTPSYTQPYQGSSVTLSTEAFLYVGTMLDGGDLSRFALLMTNCYATPSSNATDPLKYFIIQDRCPHTRDSTIQVVENGESSQGRFSVQMFRFAGNYDLVYLHCEVYLCDTMNEKCKPTCSGTRFRSGSVIDQSRVLNLGPITRKGVQATVSRAFSSLGLLKVWLPLLLSATLTLTFQ

Entity 2 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	26

Entity 3 branched

描述 description	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	748.7 kDa
来源方法 src_method	man
拷贝数 entity_count	14

Entity 4 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	13

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7. 引用文献 (1)

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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	—

分辨率 resolution	5.000 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

分辨率 resolution	5.00 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	1110345

fit	/app/data/saxs_computation/nu/9nu3/9nu3.fit
pddf	/app/data/pr_computation/nu/9nu3/9nu3.pr.out
profile	/app/data/saxs_computation/nu/9nu3/9nu3.dat

Uromodulin filament lattice in the kinked arrangement from human urine

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

冷冻电镜 EM 3D