SAXSdb — 1o29

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1o29
沉积日期 deposition_date	2003-02-18
结构标题 title	;Crystal structure of Thymidylate Synthase Complementing Protein (TM0449) from Thermotoga maritima with FAD and FdUMP at 2.0 A resolution ;
关键词 keywords	;TM0449, THYMIDYLATE SYNTHASE COMPLEMENTING PROTEIN, STRUCTURAL GENOMICS, JCSG, Joint Center for Structural Genomics, PSI, Protein Structure Initiative, 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	28.81 Å
回转半径 Rg (电子) rg_electron	28.39 Å
零角强度 I(0) i0	172741000.00
分子量 molecular_weight	107040.0 kDa
排除体积 excluded_volume	134690 Å³
包络体积 envelope_volume	154790 Å³
水化壳体积 shell_volume	43701 Å³
包络直径 envelope_diameter	101.7 Å
壳层 Rg shell_rg	37.01 Å
包络 Rg envelope_rg	28.81 Å
形状 Rg shape_rg	28.36 Å
总 Rg total_rg	29.19 Å
总原子数 total_atoms	7562
残基数 n_residues	867
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	95.7 Å
Rg (实空间) rg_real	28.77 Å
Rg 误差 (实空间) rg_real_error	0.58 Å
I(0) (实空间) i0_real	1.7270e+08
I(0) 误差 (实空间) i0_real_error	2.5070e+06
Rg (倒空间) rg_reciprocal	28.79 Å
I(0) (倒空间) i0_reciprocal	172700000.0000
解质量估计 total_estimate	0.8677
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	34.8 Å
偏度 Skewness skewness	0.410
峰度 Kurtosis kurtosis	-0.045
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	110200000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.786; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.921

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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	Thymidylate synthase thyX
分子量 formula_weight	27503.7 kDa
EC 编号 ec_number	2.1.1.-
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	7990

MGSDKIHHHHHHMKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQV

来源 Source

来源生物 organism	Thermotoga maritima
NCBI 分类编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
分子量 formula_weight	326.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	428

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6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d1o29a1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.207 — Thymidylate synthase-complementing protein Thy1
超家族 Superfamily superfamily	d.207.1 — Thymidylate synthase-complementing protein Thy1
家族 Family family	d.207.1.1 — Thymidylate synthase-complementing protein Thy1

结构域编号 domain_id	d1o29a2
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	d1o29b_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.207 — Thymidylate synthase-complementing protein Thy1
超家族 Superfamily superfamily	d.207.1 — Thymidylate synthase-complementing protein Thy1
家族 Family family	d.207.1.1 — Thymidylate synthase-complementing protein Thy1

结构域编号 domain_id	d1o29c_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.207 — Thymidylate synthase-complementing protein Thy1
超家族 Superfamily superfamily	d.207.1 — Thymidylate synthase-complementing protein Thy1
家族 Family family	d.207.1.1 — Thymidylate synthase-complementing protein Thy1

结构域编号 domain_id	d1o29d_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.207 — Thymidylate synthase-complementing protein Thy1
超家族 Superfamily superfamily	d.207.1 — Thymidylate synthase-complementing protein Thy1
家族 Family family	d.207.1.1 — Thymidylate synthase-complementing protein Thy1

CATH v4.4 (4 domains)

结构域编号 domain_id	1o29A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	170 —

结构域编号 domain_id	1o29B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	170 —

结构域编号 domain_id	1o29C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	170 —

结构域编号 domain_id	1o29D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	170 —

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7. 引用文献 (1)

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晶胞边长 a length_a	54.636 Å
晶胞边长 b length_b	116.955 Å
晶胞边长 c length_c	141.926 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 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.1938
R_free r_free	0.2323

fit	/app/data/saxs_computation/o2/1o29/1o29.fit
pddf	/app/data/pr_computation/o2/1o29/1o29.pr.out
profile	/app/data/saxs_computation/o2/1o29/1o29.dat

;Crystal structure of Thymidylate Synthase Complementing Protein (TM0449) from Thermotoga maritima with FAD and FdUMP at 2.0 A resolution ;

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