9bov

Structure of electron bifurcating Nfn-ABC complexed with NAD from Caldicellulosiruptor saccharolyticus

Method: ELECTRON MICROSCOPY D_max: 216.0 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	9bov
沉积日期 deposition_date	2024-05-06
结构标题 title	Structure of electron bifurcating Nfn-ABC complexed with NAD from Caldicellulosiruptor saccharolyticus
关键词 keywords	Electron bifurcating enzyme, Nfn-type BfuABC complex, FMN/B1/C1 bifurcation site, OXIDOREDUCTASE; OXIDOREDUCTASE
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	72.00 Å
回转半径 Rg (电子) rg_electron	72.37 Å
零角强度 I(0) i0	9042010000.00
分子量 molecular_weight	797690.0 kDa
排除体积 excluded_volume	995050 Å³
包络体积 envelope_volume	1497200 Å³
水化壳体积 shell_volume	175870 Å³
包络直径 envelope_diameter	268.3 Å
壳层 Rg shell_rg	72.22 Å
包络 Rg envelope_rg	70.19 Å
形状 Rg shape_rg	72.47 Å
总 Rg total_rg	72.02 Å
总原子数 total_atoms	55356
残基数 n_residues	7088
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	216.0 Å
Rg (实空间) rg_real	71.24 Å
Rg 误差 (实空间) rg_real_error	1.01 Å
I(0) (实空间) i0_real	8.9730e+09
I(0) 误差 (实空间) i0_real_error	1.5710e+08
Rg (倒空间) rg_reciprocal	71.47 Å
I(0) (倒空间) i0_reciprocal	9030000000.0000
解质量估计 total_estimate	0.8457
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	78.5 Å
偏度 Skewness skewness	0.431
峰度 Kurtosis kurtosis	-0.170
角度范围 angular_range	— – 0.1100 Å⁻¹
当前正则化参数 α current_alpha	0.1039
最高正则化参数 α highest_alpha	332200000.0000
实空间数据点数 n_real_points	23
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.220

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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 (9)

Entity 1 polymer

描述 description	Molybdopterin oxidoreductase
分子量 formula_weight	130025.9 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,D,J,G
原子数 atom_count	55356

MRLVRVNIDNKEIFAEEGKTILEVAHENNIEIPHLCYDKRLKPYGACGLCVVEIEGSPKLARACSTYVTDKMVIKTDSPRVRNARKMALELLLSEHRGDCRPPCVLACPAHTDCQGYVGLIANGQFREAVALIKEQLPFPASIGRVCPHPCEEACRRNMVDQPIAIAELKRFVGDIDLLDDGYIPPIKPKTGKKVAIVGGGPAGLTCAFFLAKEGHDIVVYEAMPKAGGMLRYGIPEYRLPKGILDKEIELIEKMGVQIKTNMRLGVDISLEYLRKNYDAVFLAVGAWKSSTLGCPGDSAEGVIGGIEFLRKVSMNQPVNLGQRVLVVGGGNTAMDAARTAIRLGAKEVTVLYRRTREEMPAEDIEVNEAEEEGVKFQFLVAPIEVITDGGRVRALKCQRMRLGDMDESGRRRPVPIEGAEVIFEADTIISAIGQKVRVEDVEGLELTRHGTIKVDEGTYQTSLEGVFAGGDAVTGPKIAIEAIAQGKNAARVIDSYLRGKLEPIKEPYYVKQEDLTPEDFKDRERKPRVPLKVANAEERKNNFREITSTMTEKEAIAEASRCLECGCMDYFECQLYKYVNQYDVDPQRLSGYKHKRYEPQKHPFIERNPDKCILCGLCIRVCEEVVGVCALGFVNRGFETIVKPEFGLPLEETSCISCGQCADICPTGACIGKQPVAKQVPVNTVATKTVCTFCGMGCEMLVETKGNLIFDVSPVQSNEGMLCAFGRFGIKYVNDKDRILAPLIKVNGELSKTTFDQALIETAKKLQAIRASYGKDSIAIIASQRLTNEEALLLTKLAQKLDTTVIGSFDLRESVLDRIFGLNASTNSFDEIYSTDLIVAVGKVAENHAVMGAKLKKAVELGAKLVTINNGETRADERAIATYKIDNTAFFKATIKALFEMKAVDEDYVSKIAVNLDELKDDVKNVEVTDEASEFAKIIAGAKTAMVIVDEESVSDTTIGQLANILTLTQKIGRPRCGIIKVTGLGNTQGAWDMGIRMSKEGIVKLINEGKVKAAFIVSEDPQAADKNLGEVLDKLECLIVADVFLTETGKRADVVLPLVSHVESTGTVTRADGKIQNLNLVLKPKNGLSNLDLLLKLAELFGLQYNLEKLNREMVELLQNENKYNQQILYTEGFATPDKTVHLFVSKDAPAFVEKAVFDTVKNRFEKYLQDKHLKY

来源 Source

来源生物 organism	Caldicellulosiruptor saccharolyticus
NCBI 分类编号 ncbi_taxonomy_id	44001
宿主生物 host_organism	Caldicellulosiruptor

Entity 2 polymer

描述 description	NADH dehydrogenase (Quinone)
分子量 formula_weight	63533.5 kDa
EC 编号 ec_number	1.6.99.5
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,E,K,H

MKIRVGLGSCGMAAGGNKVMECIQQELRSRNLDIPVEPTGCIGLCFFEPLVDVIDGDDVYTYGNVTPEMIPKIIESHVIGKKPLDEFIVSTSFEPYPMLKSQVRIALKNCGRINPEDIDDYIKNGGYEALKKVLTSMTPEEVIEEIKISGLRGRGGAGFPTWFKWDAARKASGDIKYVVCNADEGDPGAFMDRSILEGDPHAVLEGMTIAAYAIGAKEGYIYVRAEYPLAIKRLEIAIEQARNRNLLGNNILNTNFSFDIKLKKGAGAFVCGEETALIASIEGERGMPRLKPPFPAQSGLWGRPTNINNVETYANVPWIITNGGKAFASLGTEKSKGTKVFALAGKIKRGGLVEVPMGMSLREVIYNIGGGIKDDKAFKAVQMGGPSGGCIPADLIDTPVDYESITKTGAIMGSGGMIVMDETTCMVDIARFFLEFTCKESCGKCTYCRVGTRRMLEILDRICNGEGRDGDLELLEELAVSVKDGSLCGLGQTAPNPVLTTLRYFKDEYIAHIRDKKCPAKQCKALITYSILPEKCTGCGLCARKCPTKAITGERLKPHVIDQSKCTKCGTCMNVCRFGAVNVE

来源 Source

来源生物 organism	Caldicellulosiruptor saccharolyticus
NCBI 分类编号 ncbi_taxonomy_id	44001
宿主生物 host_organism	Caldicellulosiruptor

Entity 3 polymer

描述 description	NADH dehydrogenase (Ubiquinone), 24 kDa subunit
分子量 formula_weight	19914.1 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,F,L,I

MYMSCPECENRLASNFKNQKVDLSLLDPVLDEYKGEKSNIIAILQKTQEIYRFLPLDALNYISEKTGVKKAKIYGIATFYAQFRLKPVGKYVILQCQGTACHVNGSEEIKNALCDELNIKPGDTTEDGMFTLEEVACLGCCSLAPVMMINGETYGKLTPDKAREIIRRIYEREKNV

来源 Source

来源生物 organism	Caldicellulosiruptor saccharolyticus
NCBI 分类编号 ncbi_taxonomy_id	44001
宿主生物 host_organism	Caldicellulosiruptor

Entity 4 non-polymer

描述 description	FE2/S2 (INORGANIC) CLUSTER
分子量 formula_weight	175.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	28

Entity 6 non-polymer

描述 description	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 7 non-polymer

描述 description	FLAVIN MONONUCLEOTIDE
分子量 formula_weight	456.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 8 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 9 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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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	78470

fit	/app/data/saxs_computation/bo/9bov/9bov.fit
pddf	/app/data/pr_computation/bo/9bov/9bov.pr.out
profile	/app/data/saxs_computation/bo/9bov/9bov.dat

Structure of electron bifurcating Nfn-ABC complexed with NAD from Caldicellulosiruptor saccharolyticus

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 (9)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)