9ivp

24-mer DARPin-apoferritin scaffold in complex with the maltose binding protein

Method: ELECTRON MICROSCOPY D_max: 257.9 Å Quality: EXCELLENT

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	9ivp
沉积日期 deposition_date	2024-07-24
最后修订 last_revision	2025-06-04
结构标题 title	24-mer DARPin-apoferritin scaffold in complex with the maltose binding protein
关键词 keywords	DARPin, apoferritin, scaffold, maltose binding protein, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC 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	99.17 Å
回转半径 Rg (电子) rg_electron	99.25 Å
零角强度 I(0) i0	43429800000.00
分子量 molecular_weight	1810500.0 kDa
排除体积 excluded_volume	2275000 Å³
包络体积 envelope_volume	3902900 Å³
水化壳体积 shell_volume	333350 Å³
包络直径 envelope_diameter	306.0 Å
壳层 Rg shell_rg	95.00 Å
包络 Rg envelope_rg	94.23 Å
形状 Rg shape_rg	99.30 Å
总 Rg total_rg	99.05 Å
总原子数 total_atoms	127848
残基数 n_residues	16368
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	257.9 Å
Rg (实空间) rg_real	96.80 Å
Rg 误差 (实空间) rg_real_error	0.29 Å
I(0) (实空间) i0_real	4.1600e+10
I(0) 误差 (实空间) i0_real_error	6.8430e+08
Rg (倒空间) rg_reciprocal	101.70 Å
I(0) (倒空间) i0_reciprocal	43810000000.0000
解质量估计 total_estimate	0.9063
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	112.9 Å
偏度 Skewness skewness	0.125
峰度 Kurtosis kurtosis	-0.485
角度范围 angular_range	— – 0.0800 Å⁻¹
当前正则化参数 α current_alpha	1.0090
最高正则化参数 α highest_alpha	96040000000.0000
实空间数据点数 n_real_points	17
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.978; Stabil: 0.958; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.000

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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 (2)

Entity 1 polymer

描述 description	DARPin,Ferritin heavy chain, N-terminally processed
分子量 formula_weight	41047.1 kDa
来源方法 src_method	man
拷贝数 entity_count	24

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,E,G,I,K,M,O,Q,S,V,X,Z,BA,DA,FA,HA,JA,LA,NA,PA,RA,TA,VA
原子数 atom_count	128520

MGHHHHHHGPGSAKEEILEEIKKAKQEIAGGGGGSELGKELLEAARAGQDDEVRILMARGAEVNAADNTGTTPLHLAAYSGHLEIVEVLLKYGAEVNAADVFGYTPLHLAAYWGHLEIVEVLLKNGADVNARDSDGMTPLHLAAKWGHLEIVEVLLRYGADVEAQDKFGKTPFDLAIDNGNEDIAEVLQALLAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGAISLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHKLATDCNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGSGSGAEIEQAKKEIAYLIKK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Maltodextrin-binding protein
分子量 formula_weight	45694.2 kDa
来源方法 src_method	man
拷贝数 entity_count	24

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,D,F,H,J,L,N,P,R,T,W,Y,AA,CA,EA,GA,IA,KA,MA,OA,QA,SA,UA,WA

MGSSHHHHHHSSGLVPRGSHMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNSSSNNNNNNNNNNLGIEGRENLYFQGGS

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

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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	3.00 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	91926

fit	/app/data/saxs_computation/iv/9ivp/9ivp.fit
pddf	/app/data/pr_computation/iv/9ivp/9ivp.pr.out
profile	/app/data/saxs_computation/iv/9ivp/9ivp.dat

24-mer DARPin-apoferritin scaffold in complex with the maltose binding protein

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 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)