SAXSdb — 8f3d

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8f3d
沉积日期 deposition_date	2022-11-09
结构标题 title	3-methylcrotonyl-CoA carboxylase in filament, beta-subunit centered
关键词 keywords	enzyme, multienzyme, multi-enzyme, biotin-dependent, leucine catabolism, PROTEIN FIBRIL, LIGASE; LIGASE
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	69.36 Å
回转半径 Rg (电子) rg_electron	69.60 Å
零角强度 I(0) i0	9536380000.00
分子量 molecular_weight	822550.0 kDa
排除体积 excluded_volume	1028100 Å³
包络体积 envelope_volume	1649200 Å³
水化壳体积 shell_volume	195130 Å³
包络直径 envelope_diameter	247.5 Å
壳层 Rg shell_rg	73.07 Å
包络 Rg envelope_rg	69.11 Å
形状 Rg shape_rg	69.60 Å
总 Rg total_rg	69.63 Å
总原子数 total_atoms	57846
残基数 n_residues	7464
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	259.5 Å
Rg (实空间) rg_real	73.34 Å
Rg 误差 (实空间) rg_real_error	1.65 Å
I(0) (实空间) i0_real	9.6170e+09
I(0) 误差 (实空间) i0_real_error	1.5970e+08
Rg (倒空间) rg_reciprocal	68.83 Å
I(0) (倒空间) i0_reciprocal	9524000000.0000
解质量估计 total_estimate	0.8289
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	79.0 Å
偏度 Skewness skewness	0.717
峰度 Kurtosis kurtosis	0.314
角度范围 angular_range	— – 0.1150 Å⁻¹
当前正则化参数 α current_alpha	0.9130
最高正则化参数 α highest_alpha	1000000000.0000
实空间数据点数 n_real_points	24
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.564; Stabil: 0.862; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.534

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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	3-methylcrotonyl-CoA carboxylase beta-subunit
分子量 formula_weight	76468.5 kDa
EC 编号 ec_number	6.4.1.4
来源方法 src_method	nat
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	57846

MDKTHVLRNTTRGMFRTSMMRVLGRPGSLSVTASAGGTACVPMAALLRRSATPAAASATAASAMSALWCTRCFESSSAGSPPKVSDAGMKERSTQEPCVAATPTPSDTAATLAAAATPAPAAPIKSKGVDYARLYAHHPIDYERSTSKSPNILRLPANTSDPTYQENMARMEGLVEQLRARVRYVQAGGVVPEEEAAKAGVSISSIEADDRVRKLHLSRGKMLARDRIERLIDPGTRFLELSQLAGWDLYWDDKKKEYERCYSGGIVTGIGLVNGVRCMLVANDATVKGGTYYPITVKKHLRAQKIAEQNHLPCIYLVDSGGANLSRQDDVFPDEQHFGRIFYNEAQMSIKSISQIAVVMGSCTAGGAYVPAMADENIIVARNGTIFLGGPPLVLAATGEKVSSEELGGADVHCRISGVGDHYATDDLHALYLARRAVANLNLKEHNEARNPTDVKPVPPLYDPRELGGFIPDMLSDVVKSFDVRAIIARIVDGSRFDEFKALYGNTLVCGFARIEGMQVGIIANQGILYSESALKGAHFIGLCTQRNVPLLFLQNITGFMVGKKYEEGGIARNGARLVMAVSSAPVPKVTVLIGGSYGAGNYGMCGRAFEPRFLFMWPNARISVMGGTQAATVLTLTNRNLKNASEAEIAAFKDKVKKKYEKEGSCYYSTARLWDDGVIAPEDTRVVVAEALRATRLAPMEKRERV

Entity 2 polymer

描述 description	3-methylcrotonyl-CoA carboxylase alpha-subunit
分子量 formula_weight	76283.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H,I,J,K,L,M

MLRYTGLWRERKVEKLLVANRGEIACRVFRTCREMHIRTVALFCEAERNAKHVAEADEAVCIGPPPAVNSYLRGEHIISVAKQLNVDAIHPGYGFLSENASFADAITRSGIEFIGPPASAISLMGSKSESKRIMEAAGVPVVPGYYGENQNVSFLAEEAKKVGFPILIKAVSGGGGKGMKIVERPEDFTFMLESAKREATNFFKDDRVILERYVKRSRHIECQIFFDKHGRGVFFFERDCSVQRRYQKVLEEAPAPHLSMETRQRIGEVALQAAKAVGYVGAGTVEFIFDTSTGEFYFMEMNTRLQVEHPVTEEVCRIKGAPLDLVKLQIKTAMGKPLTFSQEDVTLVGSCIEARVYAESPERGFLPESGPLTFIREPFQGVRGPARTRLDTGFREGDNVLIHYDPMLAKVISWGRSREEALRGLRQALGEYKVAGINTNIEFLKRCCETPEFARGGVTTNFISEHESQLLKSPVVTPEVAAMAATAWLLNRCDNWRGAFRLNSDTNATVHFYIDDHPVEVRLHTEGANYHKIFFSVWDHDGSFEVCSGPVTSKHRDQKSIVNDFTFLFENGMHHTVLAVATEGDVTVIGSFGLHQLRLLPLTDGFGDSSTAGGTSTKIVSPMPGKVSKLLVKSGDLVEKGQVLVIVEAMKMEHPVRALQDGRVSFLVKEGEVVGGDHVLATVAEEE

Entity 3 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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6. 折叠分类 (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

结构域编号 domain_id	8f3dH01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	20 — ATP-grasp fold, B domain

结构域编号 domain_id	8f3dI01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	20 — ATP-grasp fold, B domain

结构域编号 domain_id	8f3dJ01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	20 — ATP-grasp fold, B domain

结构域编号 domain_id	8f3dK01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	20 — ATP-grasp fold, B domain

结构域编号 domain_id	8f3dL01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	20 — ATP-grasp fold, B domain

结构域编号 domain_id	8f3dM01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	20 — ATP-grasp fold, B domain

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7. 引用文献 (2)

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分辨率 resolution	3.40 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	13250

fit	/app/data/saxs_computation/f3/8f3d/8f3d.fit
pddf	/app/data/pr_computation/f3/8f3d/8f3d.pr.out
profile	/app/data/saxs_computation/f3/8f3d/8f3d.dat

3-methylcrotonyl-CoA carboxylase in filament, beta-subunit centered

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 (3)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

6. 折叠分类 (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)