SAXSdb — 1l6r

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1l6r
沉积日期 deposition_date	2002-03-13
结构标题 title	Crystal Structure of Thermoplasma acidophilum 0175 (APC0014)
关键词 keywords	;Structural Genomics, Hypothetical protein, putative hydroLase, Midwest Center for Structural Genomics, MCSG, PSI, Protein Structure Initiative, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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	23.65 Å
回转半径 Rg (电子) rg_electron	22.73 Å
零角强度 I(0) i0	43514700.00
分子量 molecular_weight	51056.0 kDa
排除体积 excluded_volume	63861 Å³
包络体积 envelope_volume	74470 Å³
水化壳体积 shell_volume	26788 Å³
包络直径 envelope_diameter	72.0 Å
壳层 Rg shell_rg	30.06 Å
包络 Rg envelope_rg	22.79 Å
形状 Rg shape_rg	22.72 Å
总 Rg total_rg	23.60 Å
总原子数 total_atoms	3582
残基数 n_residues	450
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	71.0 Å
Rg (实空间) rg_real	23.50 Å
Rg 误差 (实空间) rg_real_error	0.31 Å
I(0) (实空间) i0_real	4.3510e+07
I(0) 误差 (实空间) i0_real_error	5.3720e+05
Rg (倒空间) rg_reciprocal	23.53 Å
I(0) (倒空间) i0_reciprocal	43520000.0000
解质量估计 total_estimate	0.9128
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	28.8 Å
偏度 Skewness skewness	0.100
峰度 Kurtosis kurtosis	-0.555
角度范围 angular_range	— – 0.3350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7743000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.990

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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	HYPOTHETICAL PROTEIN TA0175
分子量 formula_weight	25603.0 kDa
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	4461

GSHMIRLAAIDVDGNLTDRDRLISTKAIESIRSAEKKGLTVSLLSGNVIPVVYALKIFLGINGPVFGENGGIMFDNDGSIKKFFSNEGTNKFLEEMSKRTSMRSILTNRWREASTGFDIDPEDVDYVRKEAESRGFVIFYSGYSWHLMNRGEDKAFAVNKLKEMYSLEYDEILVIGDSNNDMPMFQLPVRKACPANATDNIKAVSDFVSDYSYGEEIGQIFKHFELM

来源 Source

来源生物 organism	Thermoplasma acidophilum
NCBI 分类编号 ncbi_taxonomy_id	2303
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 3 non-polymer

描述 description	FORMIC ACID
分子量 formula_weight	46.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	715

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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	d1l6ra1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.108 — HAD-like
超家族 Superfamily superfamily	c.108.1 — HAD-like
家族 Family family	c.108.1.10 — Predicted hydrolases Cof

结构域编号 domain_id	d1l6ra2
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	d1l6rb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.108 — HAD-like
超家族 Superfamily superfamily	c.108.1 — HAD-like
家族 Family family	c.108.1.10 — Predicted hydrolases Cof

结构域编号 domain_id	d1l6rb2
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 (4 domains)

结构域编号 domain_id	1l6rA01
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	1000 — HAD superfamily/HAD-like

结构域编号 domain_id	1l6rA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1070 — Hypothetical Protein Ta0175; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1l6rB01
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	1000 — HAD superfamily/HAD-like

结构域编号 domain_id	1l6rB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1070 — Hypothetical Protein Ta0175; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	88.240 Å
晶胞边长 b length_b	99.244 Å
晶胞边长 c length_c	113.781 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	I 2 2 2
空间群编号 int_tables_number	23
晶系 crystal_system	—

分辨率 resolution	1.400 Å
最低分辨率 resolution_low	38.000 Å
R 因子 r_factor	0.1730
R_work r_work	0.1710
R_free r_free	0.1950

fit	/app/data/saxs_computation/l6/1l6r/1l6r.fit
pddf	/app/data/pr_computation/l6/1l6r/1l6r.pr.out
profile	/app/data/saxs_computation/l6/1l6r/1l6r.dat

Crystal Structure of Thermoplasma acidophilum 0175 (APC0014)

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