SAXSdb — 8jxm

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8jxm
沉积日期 deposition_date	2023-06-30
结构标题 title	Human 3-methylcrotonyl-CoA carboxylase in BCCP-H2 state with MCoA
关键词 keywords	MCC, Mitochondrial, CYTOSOLIC PROTEIN; CYTOSOLIC 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	64.35 Å
回转半径 Rg (电子) rg_electron	64.37 Å
零角强度 I(0) i0	7744090000.00
分子量 molecular_weight	740180.0 kDa
排除体积 excluded_volume	925070 Å³
包络体积 envelope_volume	1389300 Å³
水化壳体积 shell_volume	175420 Å³
包络直径 envelope_diameter	224.2 Å
壳层 Rg shell_rg	69.33 Å
包络 Rg envelope_rg	63.90 Å
形状 Rg shape_rg	64.35 Å
总 Rg total_rg	64.52 Å
总原子数 total_atoms	51993
残基数 n_residues	6678
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	202.6 Å
Rg (实空间) rg_real	64.48 Å
Rg 误差 (实空间) rg_real_error	1.23 Å
I(0) (实空间) i0_real	7.7410e+09
I(0) 误差 (实空间) i0_real_error	1.4730e+08
Rg (倒空间) rg_reciprocal	64.19 Å
I(0) (倒空间) i0_reciprocal	7739000000.0000
解质量估计 total_estimate	0.8318
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	76.0 Å
偏度 Skewness skewness	0.535
峰度 Kurtosis kurtosis	0.082
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	0.0009
最高正则化参数 α highest_alpha	793900000.0000
实空间数据点数 n_real_points	25
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.323

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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	Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
分子量 formula_weight	61406.0 kDa
EC 编号 ec_number	6.4.1.4
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	K,A,C,H,E,J
原子数 atom_count	51993

MWAVLRLALRPCARASPAGPRAYHGDSVASLGTQPDLGSALYQENYKQMKALVNQLHERVEHIKLGGGEKARALHISRGKLLPRERIDNLIDPGSPFLELSQFAGYQLYDNEEVPGGGIITGIGRVSGVECMIIANDATVKGGAYYPVTVKKQLRAQEIAMQNRLPCIYLVDSGGAYLPRQADVFPDRDHFGRTFYNQAIMSSKNIAQIAVVMGSCTAGGAYVPAMADENIIVRKQGTIFLAGPPLVKAATGEEVSAEDLGGADLHCRKSGVSDHWALDDHHALHLTRKVVRNLNYQKKLDVTIEPSEEPLFPADELYGIVGANLKRSFDVREVIARIVDGSRFTEFKAFYGDTLVTGFARIFGYPVGIVGNNGVLFSESAKKGTHFVQLCCQRNIPLLFLQNITGFMVGREYEAEGIAKDGAKMVAAVACAQVPKITLIIGGSYGAGNYGMCGRAYSPRFLYIWPNARISVMGGEQAANVLATITKDQRAREGKQFSSADEAALKEPIIKKFEEEGNPYYSSARVWDDGIIDPADTRLVLGLSFSAALNAPIEKTDFGIFRM

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	Homo sapiens

Entity 2 polymer

描述 description	Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
分子量 formula_weight	80584.0 kDa
EC 编号 ec_number	6.4.1.4
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	L,B,F,G,I,M

MAAASAVSVLLVAAERNRWHRLPSLLLPPRTWVWRQRTMKYTTATGRNITKVLIANRGEIACRVMRTAKKLGVQTVAVYSEADRNSMHVDMADEAYSIGPAPSQQSYLSMEKIIQVAKTSAAQAIHPGCGFLSENMEFAELCKQEGIIFIGPPPSAIRDMGIKSTSKSIMAAAGVPVVEGYHGEDQSDQCLKEHARRIGYPVMIKAVRGGGGKGMRIVRSEQEFQEQLESARREAKKSFNDDAMLIEKFVDTPRHVEVQVFGDHHGNAVYLFERDCSVQRRHQKIIEEAPAPGIKSEVRKKLGEAAVRAAKAVNYVGAGTVEFIMDSKHNFCFMEMNTRLQVEHPVTEMITGTDLVEWQLRIAAGEKIPLSQEEITLQGHAFEARIYAEDPSNNFMPVAGPLVHLSTPRADPSTRIETGVRQGDEVSVHYDPMIAKLVVWAADRQAALTKLRYSLRQYNIVGLHTNIDFLLNLSGHPEFEAGNVHTDFIPQHHKQLLLSRKAAAKESLCQAALGLILKEKAMTDTFTLQAHDQFSPFSSSSGRRLNISYTRNMTLKDGKNNVAIAVTYNHDGSYSMQIEDKTFQVLGNLYSEGDCTYLKCSVNGVASKAKLIILENTIYLFSKEGSIEIDIPVPKYLSSVSSQETQGGPLAPMTGTIEKVFVKAGDKVKAGDSLMVMIAMKMEHTIKSPKDGTVKKVFYREGAQANRHTPLVEFEEEESDKRESE

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	Homo sapiens

Entity 3 non-polymer

描述 description	;~{S}-[2-[3-[[(2~{R})-4-[[[(2~{S},3~{S},4~{S},5~{S})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-methylbut-2-enethioate ;
分子量 formula_weight	849.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 4 non-polymer

描述 description	5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
分子量 formula_weight	228.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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7. 引用文献 (1)

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分辨率 resolution	3.49 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	44531

fit	/app/data/saxs_computation/jx/8jxm/8jxm.fit
pddf	/app/data/pr_computation/jx/8jxm/8jxm.pr.out
profile	/app/data/saxs_computation/jx/8jxm/8jxm.dat

Human 3-methylcrotonyl-CoA carboxylase in BCCP-H2 state with MCoA

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)