SAXSdb — 1rje

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1rje
沉积日期 deposition_date	2003-11-19
结构标题 title	Structure of PPM1, a leucine carboxy methyltransferase involved in the regulation of protein phosphatase 2A activity
关键词 keywords	SAM dependent methyltransferase, 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	33.80 Å
回转半径 Rg (电子) rg_electron	32.69 Å
零角强度 I(0) i0	206522000.00
分子量 molecular_weight	115690.0 kDa
排除体积 excluded_volume	145100 Å³
包络体积 envelope_volume	181420 Å³
水化壳体积 shell_volume	45768 Å³
包络直径 envelope_diameter	115.5 Å
壳层 Rg shell_rg	40.00 Å
包络 Rg envelope_rg	32.51 Å
形状 Rg shape_rg	32.69 Å
总 Rg total_rg	33.22 Å
总原子数 total_atoms	8104
残基数 n_residues	990
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	106.4 Å
Rg (实空间) rg_real	34.35 Å
Rg 误差 (实空间) rg_real_error	0.27 Å
I(0) (实空间) i0_real	2.0330e+08
I(0) 误差 (实空间) i0_real_error	2.3770e+06
Rg (倒空间) rg_reciprocal	33.78 Å
I(0) (倒空间) i0_reciprocal	206500000.0000
解质量估计 total_estimate	0.7074
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	0
主峰位置 r_peak_primary	— Å
偏度 Skewness skewness	0.263
峰度 Kurtosis kurtosis	-0.504
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	3.5610
最高正则化参数 α highest_alpha	132700000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.954; Stabil: 0.918; Sysdev: 0.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.632

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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	carboxy methyl transferase for protein phosphatase 2A catalytic subunit
分子量 formula_weight	38567.4 kDa
EC 编号 ec_number	2.1.1.-
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	9100

MERIIQQTDYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQWHHHHHH

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	3

Entity 4 non-polymer

描述 description	BETA-MERCAPTOETHANOL
分子量 formula_weight	78.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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	990

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6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1rjea1
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.66.1.37 — Leucine carboxy methyltransferase Ppm1

结构域编号 domain_id	d1rjea2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1rjeb1
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.66.1.37 — Leucine carboxy methyltransferase Ppm1

结构域编号 domain_id	d1rjeb2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1rjec1
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.66.1.37 — Leucine carboxy methyltransferase Ppm1

结构域编号 domain_id	d1rjec2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

结构域编号 domain_id	1rjeA00
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	1rjeB00
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	1rjeC00
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	110.747 Å
晶胞边长 b length_b	110.747 Å
晶胞边长 c length_c	165.613 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	120.00 °
晶胞分子数 Z z_pdb	18

空间群 space_group	P 65
空间群编号 int_tables_number	170
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	24.470 Å
R 因子 r_factor	0.1614
R_work r_work	0.1588
R_free r_free	0.2103

fit	/app/data/saxs_computation/rj/1rje/1rje.fit
pddf	/app/data/pr_computation/rj/1rje/1rje.pr.out
profile	/app/data/saxs_computation/rj/1rje/1rje.dat

Structure of PPM1, a leucine carboxy methyltransferase involved in the regulation of protein phosphatase 2A activity

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