SAXSdb — 2dsj

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2dsj
沉积日期 deposition_date	2006-06-30
结构标题 title	Crystal structure of project ID TT0128 from Thermus thermophilus HB8
关键词 keywords	;pyrimidine-nucleoside phosphorylase, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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	36.52 Å
回转半径 Rg (电子) rg_electron	36.35 Å
零角强度 I(0) i0	125756000.00
分子量 molecular_weight	90804.0 kDa
排除体积 excluded_volume	114220 Å³
包络体积 envelope_volume	148360 Å³
水化壳体积 shell_volume	36433 Å³
包络直径 envelope_diameter	115.7 Å
壳层 Rg shell_rg	39.98 Å
包络 Rg envelope_rg	35.78 Å
形状 Rg shape_rg	36.37 Å
总 Rg total_rg	36.50 Å
总原子数 total_atoms	6386
残基数 n_residues	846
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	109.2 Å
Rg (实空间) rg_real	36.81 Å
Rg 误差 (实空间) rg_real_error	0.85 Å
I(0) (实空间) i0_real	1.2580e+08
I(0) 误差 (实空间) i0_real_error	1.8380e+06
Rg (倒空间) rg_reciprocal	36.64 Å
I(0) (倒空间) i0_reciprocal	125700000.0000
解质量估计 total_estimate	0.7987
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	33.0 Å
偏度 Skewness skewness	0.419
峰度 Kurtosis kurtosis	-0.750
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	17410000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.861; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.799; Smooth: 0.004

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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	Pyrimidine-nucleoside (Thymidine) phosphorylase
分子量 formula_weight	45437.4 kDa
EC 编号 ec_number	2.4.2.2
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	7225

MNPVAFIREKREGKKHRREDLEAFLLGYLRDEVPDYQVSAWLMAAFLRGLDPEETLWLTETMARSGKVLDLSGLPHPVDKHSSGGVGDKVSLVVGPILAASGCTFAKMSGRGLAHTGGTIDKLESVPGWRGEMTEAEFLERARRVGLVIAAQSPDLAPLDGKLYALRDVTATVESVPLIASSIMSKKLAAGARSIVLDVKVGRGAFMKTLEEARLLAKTMVAIGQGAGRRVRALLTSMEAPLGRAVGNAIEVREAIEALKGEGPGDLLEVALALAEEALRLEGLDPALARKALEGGAALEKFRAFLEAQGGDPRAVEDFSLLPLAEEHPLRAEREGVVREVDAYKVGLAVLALGGGRKRKGEPIDHGVGVYLLKKPGDRVERGEALALVYHRRRGLEEALGHLREAYALGEEAHPAPLVLEAI

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	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	830

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6. 折叠分类 (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

结构域编号 domain_id	2dsjA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C

结构域编号 domain_id	2dsjA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

结构域编号 domain_id	2dsjA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
同源超家族 H-superfamily homologous superfamily	30 — Pyrimidine nucleoside phosphorylase-like, C-terminal domain

结构域编号 domain_id	2dsjB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C

结构域编号 domain_id	2dsjB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

结构域编号 domain_id	2dsjB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
同源超家族 H-superfamily homologous superfamily	30 — Pyrimidine nucleoside phosphorylase-like, C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	58.828 Å
晶胞边长 b length_b	76.234 Å
晶胞边长 c length_c	103.862 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	91.26 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	1.800 Å
最低分辨率 resolution_low	35.780 Å
R 因子 r_factor	0.1980
R_work r_work	0.1980
R_free r_free	0.2220

fit	/app/data/saxs_computation/ds/2dsj/2dsj.fit
pddf	/app/data/pr_computation/ds/2dsj/2dsj.pr.out
profile	/app/data/saxs_computation/ds/2dsj/2dsj.dat

Crystal structure of project ID TT0128 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