1on9

;Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core (with hydrolyzed methylmalonyl-coenzyme a bound) ;

Method: X-RAY DIFFRACTION D_max: 133.7 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	1on9
沉积日期 deposition_date	2003-02-27
结构标题 title	;Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core (with hydrolyzed methylmalonyl-coenzyme a bound) ;
关键词 keywords	carboxyl transferase, domain duplication, multienzyme complex, transcarboxylase, TRANSFERASE; TRANSFERASE
实验方法 method	X-RAY DIFFRACTION

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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	43.12 Å
回转半径 Rg (电子) rg_electron	42.16 Å
零角强度 I(0) i0	1690520000.00
分子量 molecular_weight	334500.0 kDa
排除体积 excluded_volume	415510 Å³
包络体积 envelope_volume	506600 Å³
水化壳体积 shell_volume	92336 Å³
包络直径 envelope_diameter	146.2 Å
壳层 Rg shell_rg	52.99 Å
包络 Rg envelope_rg	41.92 Å
形状 Rg shape_rg	42.14 Å
总 Rg total_rg	42.64 Å
总原子数 total_atoms	23479
残基数 n_residues	3085
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	133.7 Å
Rg (实空间) rg_real	42.85 Å
Rg 误差 (实空间) rg_real_error	1.02 Å
I(0) (实空间) i0_real	1.6910e+09
I(0) 误差 (实空间) i0_real_error	3.0260e+07
Rg (倒空间) rg_reciprocal	43.12 Å
I(0) (倒空间) i0_reciprocal	1691000000.0000
解质量估计 total_estimate	0.8977
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	57.8 Å
偏度 Skewness skewness	0.081
峰度 Kurtosis kurtosis	-0.570
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	533800000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.947

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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 (5)

Entity 1 polymer

描述 description	Methylmalonyl-CoA carboxyltransferase 12S subunit
分子量 formula_weight	56327.5 kDa
EC 编号 ec_number	2.1.3.1
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	26869

AENNNLKLASTMEGRVEQLAEQRQVIEAGGGERRVEKQHSQGKQTARERLNNLLDPHSFDEVGAFRKHRTTLFGMDKAVVPADGVVTGRGTILGRPVHAASQDFTVMGGSAGETQSTKVVETMEQALLTGTPFLFFYDSGGARIQEGIDSLSGYGKMFFANVKLSGVVPQIAIIAGPCAGGASYSPALTDFIIMTKKAHMFITGPQVIKSVTGEDVTADELGGAEAHMAISGNIHFVAEDDDAAELIAKKLLSFLPQNNTEEASFVNPNNDVSPNTELRDIVPIDGKKGYDVRDVIAKIVDWGDYLEVKAGYATNLVTAFARVNGRSVGIVANQPSVMSGCLDINASDKAAEFVNFCDSFNIPLVQLVDVPGFLPGVQQEYGGIIRHGAKMLYAYSEATVPKITVVLRKAYGGSYLAMCNRDLGADAVYAWPSAEIAVMGAEGAANVIFRKEIKAADDPDAMRAEKIEEYQNAFNTPYVAAARGQVDDVIDPADTRRKIASALEMYATKRQTRPAKKHGNFPC

来源 Source

来源生物 organism	Propionibacterium freudenreichii
NCBI 分类编号 ncbi_taxonomy_id	1744
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	CADMIUM ION
分子量 formula_weight	112.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	METHYLMALONYL-COENZYME A
分子量 formula_weight	867.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 4 non-polymer

描述 description	(4S)-2-METHYL-2,4-PENTANEDIOL
分子量 formula_weight	118.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	3390

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1on9a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

结构域编号 domain_id	d1on9a2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

结构域编号 domain_id	d1on9b1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

结构域编号 domain_id	d1on9b2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

结构域编号 domain_id	d1on9c1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

结构域编号 domain_id	d1on9c2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

结构域编号 domain_id	d1on9d1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

结构域编号 domain_id	d1on9d2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

结构域编号 domain_id	d1on9e1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

结构域编号 domain_id	d1on9e2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

结构域编号 domain_id	d1on9f1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

结构域编号 domain_id	d1on9f2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.4 — Biotin dependent carboxylase carboxyltransferase domain

CATH v4.4 (12 domains)

结构域编号 domain_id	1on9A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1on9A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1on9B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1on9B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1on9C01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1on9C02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1on9D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1on9D02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1on9E01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1on9E02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1on9F01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1on9F02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

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7. 引用文献 (1)

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晶胞边长 a length_a	113.810 Å
晶胞边长 b length_b	200.020 Å
晶胞边长 c length_c	145.900 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	102.97 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	29.550 Å
R 因子 r_factor	0.1520
R_work r_work	0.1520
R_free r_free	0.1980

fit	/app/data/saxs_computation/on/1on9/1on9.fit
pddf	/app/data/pr_computation/on/1on9/1on9.pr.out
profile	/app/data/saxs_computation/on/1on9/1on9.dat