SAXSdb — 2hry

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2hry
沉积日期 deposition_date	2006-07-20
结构标题 title	T. maritima PurL complexed with AMPPCP
关键词 keywords	beta barrel; alpha-beta structure, ligase; LIGASE
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	24.89 Å
回转半径 Rg (电子) rg_electron	24.25 Å
零角强度 I(0) i0	65098500.00
分子量 molecular_weight	63567.0 kDa
排除体积 excluded_volume	79822 Å³
包络体积 envelope_volume	89530 Å³
水化壳体积 shell_volume	30373 Å³
包络直径 envelope_diameter	85.5 Å
壳层 Rg shell_rg	32.05 Å
包络 Rg envelope_rg	24.49 Å
形状 Rg shape_rg	24.26 Å
总 Rg total_rg	25.03 Å
总原子数 total_atoms	4467
残基数 n_residues	575
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	86.8 Å
Rg (实空间) rg_real	24.87 Å
Rg 误差 (实空间) rg_real_error	0.78 Å
I(0) (实空间) i0_real	6.5100e+07
I(0) 误差 (实空间) i0_real_error	8.7870e+05
Rg (倒空间) rg_reciprocal	24.87 Å
I(0) (倒空间) i0_reciprocal	65100000.0000
解质量估计 total_estimate	0.7726
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	28.9 Å
偏度 Skewness skewness	0.392
峰度 Kurtosis kurtosis	-0.195
角度范围 angular_range	— – 0.3200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	24790000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.700; Stabil: 0.993; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.000

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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	Phosphoribosylformylglycinamidine synthase II
分子量 formula_weight	65976.5 kDa
EC 编号 ec_number	6.3.5.3
突变 mutation	His72Ala
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	4703

MKLRYLNILKEKLGREPTFVELQAFSVMWSEHCGYSHTKKYIRRLPKTGFEGNAGVVNLDDYYSVAFKIESANHPSAIEPYNGAATGVGGIIRDVLAMGARPTAIFDSLHMSRIIDGIIEGIADYGNSIGVPTVGGELRISSLYAHNPLVNVLAAGVVRNDMLVDSKASRPGQVIVIFGGATGRDGIHGASFASEDLTGDKATKLSIQVGDPFAEKMLIEAFLEMVEEGLVEGAQDLGAGGVLSATSELVAKGNLGAIVHLDRVPLREPDMEPWEILISESQERMAVVTSPQKASRILEIARKHLLFGDVVAEVIEEPVYRVMYRNDLVMEVPVQLLANAPEEDIVEYTPGKIPEFKRVEFEEVNAREVFEQYDHMVGTDTVVPPGFGAAVMRIKRDGGYSLVTHSRADLALQDTYWGTLIAVLESVRKTLSVGAEPLAITNCVNYGDPDVDPVGLSAMMTALKNACEFSGVPVASGNASLYNTYQGKPIPPTLVVGMLGKVNPQKVAKPKPSKVFAVGWNDFELEREKELWRAIRKLSEEGAFILSSSQLLTRTHVETFREYGLKIEVKLPEVRPAHQMVLVFSERTPVVDVPVKEIGTLSR

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	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
分子量 formula_weight	505.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	236

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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	d2hrya1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.4 — PurM N-terminal domain-like
家族 Family family	d.79.4.1 — PurM N-terminal domain-like

结构域编号 domain_id	d2hrya2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.4 — PurM N-terminal domain-like
家族 Family family	d.79.4.1 — PurM N-terminal domain-like

结构域编号 domain_id	d2hrya3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.139 — PurM C-terminal domain-like
超家族 Superfamily superfamily	d.139.1 — PurM C-terminal domain-like
家族 Family family	d.139.1.1 — PurM C-terminal domain-like

结构域编号 domain_id	d2hrya4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.139 — PurM C-terminal domain-like
超家族 Superfamily superfamily	d.139.1 — PurM C-terminal domain-like
家族 Family family	d.139.1.1 — PurM C-terminal domain-like

CATH v4.4 (4 domains)

结构域编号 domain_id	2hryA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	650 — Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — PurM-like C-terminal domain

结构域编号 domain_id	2hryA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	10 — PurM-like, N-terminal domain

结构域编号 domain_id	2hryA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	10 — PurM-like, N-terminal domain

结构域编号 domain_id	2hryA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1670 — Formylglycinamide ribonucleotide amidotransferase, C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	56.617 Å
晶胞边长 b length_b	69.997 Å
晶胞边长 c length_c	133.476 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	4

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	2.800 Å
最低分辨率 resolution_low	19.880 Å
R 因子 r_factor	0.1850
R_work r_work	0.1850
R_free r_free	0.2830

fit	/app/data/saxs_computation/hr/2hry/2hry.fit
pddf	/app/data/pr_computation/hr/2hry/2hry.pr.out
profile	/app/data/saxs_computation/hr/2hry/2hry.dat

T. maritima PurL complexed with AMPPCP

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