SAXSdb — 2cwd

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2cwd
沉积日期 deposition_date	2005-06-20
结构标题 title	Crystal Structure of TT1001 protein from Thermus thermophilus HB8
关键词 keywords	;tyrosine phosphatase, structural genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, NPPSFA, National Project on Protein Structural and Functional Analyses, Hydrolase ;; HYDROLASE
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	32.66 Å
回转半径 Rg (电子) rg_electron	32.06 Å
零角强度 I(0) i0	79719900.00
分子量 molecular_weight	69400.0 kDa
排除体积 excluded_volume	86246 Å³
包络体积 envelope_volume	110780 Å³
水化壳体积 shell_volume	29364 Å³
包络直径 envelope_diameter	108.6 Å
壳层 Rg shell_rg	38.15 Å
包络 Rg envelope_rg	31.65 Å
形状 Rg shape_rg	32.06 Å
总 Rg total_rg	32.60 Å
总原子数 total_atoms	4893
残基数 n_residues	599
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	105.4 Å
Rg (实空间) rg_real	32.66 Å
Rg 误差 (实空间) rg_real_error	0.92 Å
I(0) (实空间) i0_real	7.9720e+07
I(0) 误差 (实空间) i0_real_error	1.1610e+06
Rg (倒空间) rg_reciprocal	32.67 Å
I(0) (倒空间) i0_reciprocal	79720000.0000
解质量估计 total_estimate	0.8879
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	48.3 Å
偏度 Skewness skewness	0.188
峰度 Kurtosis kurtosis	-0.680
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	23550000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.913; 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 (3)

Entity 1 polymer

描述 description	low molecular weight phosphotyrosine protein phosphatase
分子量 formula_weight	18467.9 kDa
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	5291

MDRPVRVLFVCLGNICRSPMAEGIFRKLLKERGLEDRFEVDSAGTGAWHVGEPMDPRARRVLEEEGAYFPHVARRLTREDVLAYDHILVMDRENLEEVLRRFPEARGKVRLVLEELGGGEVQDPYYGDLEDFREVYWTLEAALQAFLDRHGSPSPAAEGRA

来源 Source

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	300852
宿主生物 host_organism	Escherichia coli BL21(DE3)

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	4

Entity 3 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	398

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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	d2cwda_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.44 — Phosphotyrosine protein phosphatases I-like
超家族 Superfamily superfamily	c.44.1 — Phosphotyrosine protein phosphatases I
家族 Family family	c.44.1.0 — automated matches

结构域编号 domain_id	d2cwdb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.44 — Phosphotyrosine protein phosphatases I-like
超家族 Superfamily superfamily	c.44.1 — Phosphotyrosine protein phosphatases I
家族 Family family	c.44.1.0 — automated matches

结构域编号 domain_id	d2cwdc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.44 — Phosphotyrosine protein phosphatases I-like
超家族 Superfamily superfamily	c.44.1 — Phosphotyrosine protein phosphatases I
家族 Family family	c.44.1.0 — automated matches

结构域编号 domain_id	d2cwdd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.44 — Phosphotyrosine protein phosphatases I-like
超家族 Superfamily superfamily	c.44.1 — Phosphotyrosine protein phosphatases I
家族 Family family	c.44.1.0 — automated matches

CATH v4.4 (4 domains)

结构域编号 domain_id	2cwdA00
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	2300 — Response regulator

结构域编号 domain_id	2cwdB00
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	2300 — Response regulator

结构域编号 domain_id	2cwdC00
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	2300 — Response regulator

结构域编号 domain_id	2cwdD00
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	2300 — Response regulator

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7. 引用文献 (1)

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晶胞边长 a length_a	98.108 Å
晶胞边长 b length_b	31.293 Å
晶胞边长 c length_c	102.605 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	98.70 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	38.040 Å
R 因子 r_factor	0.2270
R_work r_work	0.2270
R_free r_free	0.2530

fit	/app/data/saxs_computation/cw/2cwd/2cwd.fit
pddf	/app/data/pr_computation/cw/2cwd/2cwd.pr.out
profile	/app/data/saxs_computation/cw/2cwd/2cwd.dat

Crystal Structure of TT1001 protein from Thermus thermophilus HB8

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

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

Entity 3 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)