2a7s

Crystal Structure of the Acyl-CoA Carboxylase, AccD5, from Mycobacterium tuberculosis

Method: X-RAY DIFFRACTION D_max: 138.9 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	2a7s
沉积日期 deposition_date	2005-07-06
结构标题 title	Crystal Structure of the Acyl-CoA Carboxylase, AccD5, from Mycobacterium tuberculosis
关键词 keywords	;carboxylase, carboxyltransferase, acetyl-CoA carboxylase, propionyl-CoA carboxylase, Acyl-CoA Carboxylase, mycolic acid, fatty acid, polyketide, Ligase ;; LIGASE
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	44.11 Å
回转半径 Rg (电子) rg_electron	43.13 Å
零角强度 I(0) i0	1720720000.00
分子量 molecular_weight	343490.0 kDa
排除体积 excluded_volume	429330 Å³
包络体积 envelope_volume	541440 Å³
水化壳体积 shell_volume	96827 Å³
包络直径 envelope_diameter	151.5 Å
壳层 Rg shell_rg	53.72 Å
包络 Rg envelope_rg	42.86 Å
形状 Rg shape_rg	43.15 Å
总 Rg total_rg	43.44 Å
总原子数 total_atoms	24180
残基数 n_residues	3174
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	138.9 Å
Rg (实空间) rg_real	43.83 Å
Rg 误差 (实空间) rg_real_error	1.07 Å
I(0) (实空间) i0_real	1.7210e+09
I(0) 误差 (实空间) i0_real_error	3.0580e+07
Rg (倒空间) rg_reciprocal	44.11 Å
I(0) (倒空间) i0_reciprocal	1721000000.0000
解质量估计 total_estimate	0.8908
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	57.9 Å
偏度 Skewness skewness	0.112
峰度 Kurtosis kurtosis	-0.506
角度范围 angular_range	— – 0.1800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	773200000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.923

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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 (2)

Entity 1 polymer

描述 description	Probable propionyl-CoA carboxylase beta chain 5
分子量 formula_weight	59420.0 kDa
EC 编号 ec_number	6.4.1.3
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	25316

MTSVTDRSAHSAERSTEHTIDIHTTAGKLAELHKRREESLHPVGEDAVEKVHAKGKLTARERIYALLDEDSFVELDALAKHRSTNFNLGEKRPLGDGVVTGYGTIDGRDVCIFSQDATVFGGSLGEVYGEKIVKVQELAIKTGRPLIGINDGAGARIQEGVVSLGLYSRIFRNNILASGVIPQISLIMGAAAGGHVYSPALTDFVIMVDQTSQMFITGPDVIKTVTGEEVTMEELGGAHTHMAKSGTAHYAASGEQDAFDYVRELLSYLPPNNSTDAPRYQAAAPTGPIEENLTDEDLELDTLIPDSPNQPYDMHEVITRLLDDEFLEIQAGYAQNIVVGFGRIDGRPVGIVANQPTHFAGCLDINASEKAARFVRTCDCFNIPIVMLVDVPGFLPGTDQEYNGIIRRGAKLLYAYGEATVPKITVITRKAYGGAYCVMGSKDMGCDVNLAWPTAQIAVMGASGAVGFVYRQQLAEAAANGEDIDKLRLRLQQEYEDTLVNPYVAAERGYVDAVIPPSHTRGYIGTALRLLERKIAQLPPKKHGNVPL

来源 Source

来源生物 organism	Mycobacterium tuberculosis
NCBI 分类编号 ncbi_taxonomy_id	1773
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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	1136

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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	d2a7sa1
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	d2a7sa2
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	d2a7sb1
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	d2a7sb2
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	d2a7sc1
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	d2a7sc2
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	d2a7sd1
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	d2a7sd2
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	d2a7se1
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	d2a7se2
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	d2a7sf1
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	d2a7sf2
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	2a7sA01
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	2a7sA02
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	2a7sB01
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	2a7sB02
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	2a7sC01
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	2a7sC02
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	2a7sD01
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	2a7sD02
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	2a7sE01
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	2a7sE02
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	2a7sF01
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	2a7sF02
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	175.252 Å
晶胞边长 b length_b	175.252 Å
晶胞边长 c length_c	342.999 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	48

空间群 space_group	P 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	47.880 Å
R 因子 r_factor	0.1930
R_work r_work	0.1930
R_free r_free	0.2450

fit	/app/data/saxs_computation/a7/2a7s/2a7s.fit
pddf	/app/data/pr_computation/a7/2a7s/2a7s.pr.out
profile	/app/data/saxs_computation/a7/2a7s/2a7s.dat

Crystal Structure of the Acyl-CoA Carboxylase, AccD5, from Mycobacterium tuberculosis

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

精修参数 Refinement

衍射实验 Diffraction