SAXSdb — 1kpg

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1kpg
沉积日期 deposition_date	2001-12-30
结构标题 title	Crystal Structure of mycolic acid cyclopropane synthase CmaA1 complexed with SAH and CTAB
关键词 keywords	;mixed alpha beta fold, Structural Genomics, PSI, Protein Structure Initiative, TB Structural Genomics Consortium, TBSGC, 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	34.93 Å
回转半径 Rg (电子) rg_electron	34.21 Å
零角强度 I(0) i0	273539000.00
分子量 molecular_weight	133120.0 kDa
排除体积 excluded_volume	165740 Å³
包络体积 envelope_volume	204560 Å³
水化壳体积 shell_volume	48679 Å³
包络直径 envelope_diameter	110.5 Å
壳层 Rg shell_rg	41.82 Å
包络 Rg envelope_rg	33.68 Å
形状 Rg shape_rg	34.21 Å
总 Rg total_rg	34.71 Å
总原子数 total_atoms	9251
残基数 n_residues	1101
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	107.3 Å
Rg (实空间) rg_real	34.74 Å
Rg 误差 (实空间) rg_real_error	0.64 Å
I(0) (实空间) i0_real	2.7350e+08
I(0) 误差 (实空间) i0_real_error	4.7160e+06
Rg (倒空间) rg_reciprocal	34.86 Å
I(0) (倒空间) i0_reciprocal	273600000.0000
解质量估计 total_estimate	0.9053
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	50.1 Å
偏度 Skewness skewness	0.059
峰度 Kurtosis kurtosis	-0.670
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	118800000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.931

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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	CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 1
分子量 formula_weight	32966.1 kDa
EC 编号 ec_number	2.1.1.79
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	9906

MPDELKPHFANVQAHYDLSDDFFRLFLDPTQTYSCAYFERDDMTLQEAQIAKIDLALGKLGLQPGMTLLDVGCGWGATMMRAVEKYDVNVVGLTLSKNQANHVQQLVANSENLRSKRVLLAGWEQFDEPVDRIVSIGAFEHFGHERYDAFFSLAHRLLPADGVMLLHTITGLHPKEIHERGLPMSFTFARFLKFIVTEIFPGGRLPSIPMVQECASANGFTVTRVQSLQPHYAKTLDLWSAALQANKGQAIALQSEEVYERYMKYLTGCAEMFRIGYIDVNQFTCQK

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 non-polymer

描述 description	CARBONATE ION
分子量 formula_weight	60.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	S-ADENOSYL-L-HOMOCYSTEINE
分子量 formula_weight	384.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	CETYL-TRIMETHYL-AMMONIUM
分子量 formula_weight	284.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	655

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1kpga_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.18 — Mycolic acid cyclopropane synthase

结构域编号 domain_id	d1kpgb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.18 — Mycolic acid cyclopropane synthase

结构域编号 domain_id	d1kpgc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.18 — Mycolic acid cyclopropane synthase

结构域编号 domain_id	d1kpgd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.18 — Mycolic acid cyclopropane synthase

CATH v4.4 (4 domains)

结构域编号 domain_id	1kpgA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	1kpgB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	1kpgC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	1kpgD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

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7. 引用文献 (1)

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晶胞边长 a length_a	77.323 Å
晶胞边长 b length_b	77.323 Å
晶胞边长 c length_c	173.490 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	16

空间群 space_group	P 43
空间群编号 int_tables_number	78
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	29.680 Å
R 因子 r_factor	0.1910
R_work r_work	0.1910
R_free r_free	0.2330

fit	/app/data/saxs_computation/kp/1kpg/1kpg.fit
pddf	/app/data/pr_computation/kp/1kpg/1kpg.pr.out
profile	/app/data/saxs_computation/kp/1kpg/1kpg.dat

Crystal Structure of mycolic acid cyclopropane synthase CmaA1 complexed with SAH and CTAB

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