9i0h

CryoEM structure of transit-GmNifEN

Method: ELECTRON MICROSCOPY D_max: 119.7 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	9i0h
沉积日期 deposition_date	2025-01-15
结构标题 title	CryoEM structure of transit-GmNifEN
关键词 keywords	NITROGENASE COFACTOR MATURATION, PROTEIN BINDING, Metalloenzyme, Iron-Sulfur Cluster, METAL BINDING PROTEIN; METAL BINDING 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	38.02 Å
回转半径 Rg (电子) rg_electron	37.24 Å
零角强度 I(0) i0	453191000.00
分子量 molecular_weight	172930.0 kDa
排除体积 excluded_volume	216350 Å³
包络体积 envelope_volume	283240 Å³
水化壳体积 shell_volume	61910 Å³
包络直径 envelope_diameter	124.0 Å
壳层 Rg shell_rg	44.85 Å
包络 Rg envelope_rg	36.71 Å
形状 Rg shape_rg	37.20 Å
总 Rg total_rg	37.81 Å
总原子数 total_atoms	12040
残基数 n_residues	1566
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	119.7 Å
Rg (实空间) rg_real	37.82 Å
Rg 误差 (实空间) rg_real_error	0.99 Å
I(0) (实空间) i0_real	4.5320e+08
I(0) 误差 (实空间) i0_real_error	7.0040e+06
Rg (倒空间) rg_reciprocal	37.95 Å
I(0) (倒空间) i0_reciprocal	453200000.0000
解质量估计 total_estimate	0.9027
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	45.6 Å
偏度 Skewness skewness	0.149
峰度 Kurtosis kurtosis	-0.576
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	75070000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.945

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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	Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
分子量 formula_weight	100135.6 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	12046

MAKPDYYDVSECETHEKGAPKFCKKSEPGEGAERSCAYDGARVVLMPITDVIHLVHGPIACAGNSWDNRGARSSDSQLYRRGFTTEMLENDVVFGGEKKLYRAILELAERYEGQAKAMFVYATCVTAMTGDDVEAVCAAAGKKVAIPLIPVNTPGFIGDKNIGNRLAGEVLFKHVIGTAEPPVLGEYPINLIGEYNIAGDLWGMLPLFERLGIQVLSCFSGDATFEELRYAHRAKLNIIICSKSLTNLARKMQKNYGMPYLEESFYGMTDTAKALRDIARELDDAVGGLEKRIMQDRVEKLLEEEEATCRERLAPYRARLEGKRSVLFTGGVKTWSMVNALRELGVEILAAGTQNSTLEDFYRMKALMHQDARIIEDTSSAGLLQVMYDKMPDLIVAGGKTKFLALKTKTPFLDINHGRSHPYAGYEGMVTFAKQLDLTVNNPIWPVLNAKAPWEKTEEELTAAVALAAGHARACLDEDLKDSTVKVPAKNATVNPQKNSPALGATLAYLGIDQMLALLHGAQGCSTFIRLQLSRHFKEPVALNSTAMSEDTAIFGGWENLKKGLKKVIEKFSPEVVGVMTSGLTETMGDDVRSAIVHFRQEYPEHDGVPVVWASTPDYCGSLQEGYAATVEAIVRSVPEPGETIPGQVTVLPGAHLTPADVEEVRELCEAFGLDPIIVPDIANALDGHIDETVSPLSTGGVSMARIRQAGQSAATLFIGDSLAKAAEAMTERCGMPSYGFTSLTGLAQVDRFMETLAAIAGRPIPEKFRRWRSRLMDAMVDSHYQFGLKKVTVALEGDNLKTLVNFLAGMGCEIQAAIAATRVRGLDGLPARDIFVGDLEDLETAARGSDLIVANSNGRQAAAKLGIKAHLRAGLPVFDRLGAHQKMWVGYRGTMNLLFETANLFQANAGEGQKLAHN

来源 Source

来源生物 organism	Geobacter metallireducens
NCBI 分类编号 ncbi_taxonomy_id	28232
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	FeFe cofactor
分子量 formula_weight	747.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

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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	2.62 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	370821

fit	/app/data/saxs_computation/i0/9i0h/9i0h.fit
pddf	/app/data/pr_computation/i0/9i0h/9i0h.pr.out
profile	/app/data/saxs_computation/i0/9i0h/9i0h.dat