1vrg

Crystal structure of propionyl-CoA carboxylase, beta subunit (TM0716) from THERMOTOGA MARITIMA at 2.30 A resolution

Method: X-RAY DIFFRACTION D_max: 136.3 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	1vrg
沉积日期 deposition_date	2005-02-22
结构标题 title	Crystal structure of propionyl-CoA carboxylase, beta subunit (TM0716) from THERMOTOGA MARITIMA at 2.30 A resolution
关键词 keywords	;TM0716, propionyl-CoA carboxylase, beta subunit, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, 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	43.61 Å
回转半径 Rg (电子) rg_electron	42.56 Å
零角强度 I(0) i0	1641550000.00
分子量 molecular_weight	338900.0 kDa
排除体积 excluded_volume	423800 Å³
包络体积 envelope_volume	518150 Å³
水化壳体积 shell_volume	93643 Å³
包络直径 envelope_diameter	148.0 Å
壳层 Rg shell_rg	53.28 Å
包络 Rg envelope_rg	42.28 Å
形状 Rg shape_rg	42.57 Å
总 Rg total_rg	42.94 Å
总原子数 total_atoms	23610
残基数 n_residues	3012
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	136.3 Å
Rg (实空间) rg_real	43.33 Å
Rg 误差 (实空间) rg_real_error	0.81 Å
I(0) (实空间) i0_real	1.6420e+09
I(0) 误差 (实空间) i0_real_error	2.8440e+07
Rg (倒空间) rg_reciprocal	43.60 Å
I(0) (倒空间) i0_reciprocal	1642000000.0000
解质量估计 total_estimate	0.8942
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	56.8 Å
偏度 Skewness skewness	0.087
峰度 Kurtosis kurtosis	-0.546
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	577900000.0000
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: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.929

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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	propionyl-CoA carboxylase, beta subunit
分子量 formula_weight	58602.8 kDa
EC 编号 ec_number	6.4.1.2
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	25115

MGSDKIHHHHHHMSLRDKIEELKKIEKEIEQGGGPEKVEKQHRAGKLTAWERLELLLDPGTFVEIDKFVEHRNTYFGLDKVKLPRDGVITGVGEINGRKVAVFSQDFTVMGGSLGEMHAKKIVKLLDLALKMGIPVIGINDSGGARIQEGVDALAGYGEIFLRNTLASGVVPQITVIAGPCAGGAVYSPALTDFIVMVDQTARMFITGPNVIKAVTGEEISQEDLGGAMVHNQKSGNAHFLADNDEKAMSLVRTLLSYLPSNNAEEPPVEDPDTSLETPEDILDILPDNPNKGYDVRDVIKRVVDHGEFFEVQPYFAKNIVIGFARIQGKTVGIVANQPSVLAGVLDIDSSDKAARFIRFLDAFNIPILTFVDTPGYLPGVAQEHGGIIRHGAKLLYAYSEATVPKITVILRKAYGGAYIAMGSKHLGADMVLAWPSAEIAVMGPEGAANIIFKREIEASSNPEETRRKLIEEYKQQFANPYIAASRGYVDMVIDPRETRKYIMRALEVCETKVEYRPKKKHGNIPL

来源 Source

来源生物 organism	Thermotoga maritima
NCBI 分类编号 ncbi_taxonomy_id	243274
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	BICARBONATE ION
分子量 formula_weight	61.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

Entity 4 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	1439

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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	d1vrga1
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	d1vrga2
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	d1vrgb1
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	d1vrgb2
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	d1vrgc1
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	d1vrgc2
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	d1vrgd1
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	d1vrgd2
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	d1vrge1
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	d1vrge2
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	d1vrgf1
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	d1vrgf2
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	1vrgA01
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	1vrgA02
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	1vrgB01
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	1vrgB02
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	1vrgC01
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	1vrgC02
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	1vrgD01
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	1vrgD02
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	1vrgE01
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	1vrgE02
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	1vrgF01
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	1vrgF02
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	113.922 Å
晶胞边长 b length_b	162.210 Å
晶胞边长 c length_c	187.117 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	24

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	45.360 Å
R 因子 r_factor	0.1568
R_work r_work	0.1540
R_free r_free	0.2098

fit	/app/data/saxs_computation/vr/1vrg/1vrg.fit
pddf	/app/data/pr_computation/vr/1vrg/1vrg.pr.out
profile	/app/data/saxs_computation/vr/1vrg/1vrg.dat