9c6c

cryoEM structure of CRISPR associated effector, CARF-Adenosine deaminase 1, Cad1, in apo form with ATP (symmetric sites).

Method: ELECTRON MICROSCOPY D_max: 203.5 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	9c6c
沉积日期 deposition_date	2024-06-07
结构标题 title	cryoEM structure of CRISPR associated effector, CARF-Adenosine deaminase 1, Cad1, in apo form with ATP (symmetric sites).
关键词 keywords	Antiphage defense, CRISPR, Deamination, CARF-Adenosine deaminase, ATP, ANTIVIRAL PROTEIN; ANTIVIRAL 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	58.55 Å
回转半径 Rg (电子) rg_electron	58.76 Å
零角强度 I(0) i0	2195990000.00
分子量 molecular_weight	395450.0 kDa
排除体积 excluded_volume	495960 Å³
包络体积 envelope_volume	698950 Å³
水化壳体积 shell_volume	102950 Å³
包络直径 envelope_diameter	197.1 Å
壳层 Rg shell_rg	57.23 Å
包络 Rg envelope_rg	58.62 Å
形状 Rg shape_rg	58.78 Å
总 Rg total_rg	58.64 Å
总原子数 total_atoms	27808
残基数 n_residues	3516
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	203.5 Å
Rg (实空间) rg_real	58.74 Å
Rg 误差 (实空间) rg_real_error	2.67 Å
I(0) (实空间) i0_real	2.1960e+09
I(0) 误差 (实空间) i0_real_error	4.9290e+07
Rg (倒空间) rg_reciprocal	58.36 Å
I(0) (倒空间) i0_reciprocal	2195000000.0000
解质量估计 total_estimate	0.8529
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	60.3 Å
偏度 Skewness skewness	0.376
峰度 Kurtosis kurtosis	-0.517
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	128500000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.796; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.741

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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	Adenosine deaminase domain-containing protein
分子量 formula_weight	67264.9 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	27808

MSRVLLCSAGHSSMVVPEAFHAVPEGFEEVHVFTTDSEKFNPVVLNDFFHSLPNVRFSITKCHGLADILNERDFEFYQEMLWQWYLTKMPDNELPYVCLSGGIKSMSASLQKAATLFGAQSVFHVLADNNPRNIEEMFDALQKGQIHFIEMGYEPGWAALRRLKKILPINEGCSRDNFKPLISKSIEEILSNVKIMASDTGKSNQLPFPSLAILPPIAQQWLQLPLSANDGAWIQNLPKVDLHCHLGGFATSGSLLDQVRGAASEPDLIDRTFSPQEIAGWPRSHKSISLDKYMELGNANGSKLLKDKGCLIRQVELLYQSLVNDNVAYAEIRCSPNNYADKNKNRSAWVVLQDINDTFTRLITEAKQKNQFYCHVNLLVIASRKFSGDLSDISKHLALAITAMQQGEGVCRIVGVDLAGFENKETRASYYEHDFKAVHRCGLAVTAHAGENDDPEGIWQAVYSLHARRLGHALNLLEAPDLMRTVIERKIGVEMCPYANYQIKGFAPMPNFSALYPLKKYLEAGILVSVNTDNIGISGANLSENLLILADLCPGISRMDVLTIIRNSIETAFISHDFRMELLKFFDRKIYDVCLISIKN

来源 Source

来源生物 organism	Bacteroidales bacterium
NCBI 分类编号 ncbi_taxonomy_id	2030927
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 3 non-polymer

描述 description	ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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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	3.40 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	106838

fit	/app/data/saxs_computation/c6/9c6c/9c6c.fit
pddf	/app/data/pr_computation/c6/9c6c/9c6c.pr.out
profile	/app/data/saxs_computation/c6/9c6c/9c6c.dat