SAXSdb — 1wek

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1wek
沉积日期 deposition_date	2004-05-25
结构标题 title	Crystal structure of the conserved hypothetical protein TT1465 from Thermus thermophilus HB8
关键词 keywords	Rossmann fold, Structural genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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	35.11 Å
回转半径 Rg (电子) rg_electron	34.07 Å
零角强度 I(0) i0	278368000.00
分子量 molecular_weight	139640.0 kDa
排除体积 excluded_volume	176370 Å³
包络体积 envelope_volume	213460 Å³
水化壳体积 shell_volume	51152 Å³
包络直径 envelope_diameter	103.6 Å
壳层 Rg shell_rg	41.83 Å
包络 Rg envelope_rg	33.92 Å
形状 Rg shape_rg	34.08 Å
总 Rg total_rg	34.57 Å
总原子数 total_atoms	9886
残基数 n_residues	1234
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	105.7 Å
Rg (实空间) rg_real	34.97 Å
Rg 误差 (实空间) rg_real_error	0.62 Å
I(0) (实空间) i0_real	2.7840e+08
I(0) 误差 (实空间) i0_real_error	4.0460e+06
Rg (倒空间) rg_reciprocal	35.06 Å
I(0) (倒空间) i0_reciprocal	278400000.0000
解质量估计 total_estimate	0.9073
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	42.3 Å
偏度 Skewness skewness	0.136
峰度 Kurtosis kurtosis	-0.661
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	46480000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.979; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.857

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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	hypothetical protein TT1465
分子量 formula_weight	24402.6 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	10248

MPKKPLIDQLHHEDSWRLFRILAEFVEGFETLSELQVPLVSVFGSARFGEGHPAYEAGYRLGRALAEAGFGVVTGGGPGVMEAVNRGAYEAGGVSVGLNIELPHEQKPNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVLLQTEKVHRFPVFLLDRGYWEGLVRWLAFLRDQKAVGPEDLQLFRLTDEPEEVVQALKAEAPPR

来源 Source

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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	12

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	362

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1weka_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.129 — MCP/YpsA-like
超家族 Superfamily superfamily	c.129.1 — MCP/YpsA-like
家族 Family family	c.129.1.1 — MoCo carrier protein-like

结构域编号 domain_id	d1wekb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.129 — MCP/YpsA-like
超家族 Superfamily superfamily	c.129.1 — MCP/YpsA-like
家族 Family family	c.129.1.1 — MoCo carrier protein-like

结构域编号 domain_id	d1wekc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.129 — MCP/YpsA-like
超家族 Superfamily superfamily	c.129.1 — MCP/YpsA-like
家族 Family family	c.129.1.1 — MoCo carrier protein-like

结构域编号 domain_id	d1wekd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.129 — MCP/YpsA-like
超家族 Superfamily superfamily	c.129.1 — MCP/YpsA-like
家族 Family family	c.129.1.1 — MoCo carrier protein-like

结构域编号 domain_id	d1weke_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.129 — MCP/YpsA-like
超家族 Superfamily superfamily	c.129.1 — MCP/YpsA-like
家族 Family family	c.129.1.1 — MoCo carrier protein-like

结构域编号 domain_id	d1wekf_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.129 — MCP/YpsA-like
超家族 Superfamily superfamily	c.129.1 — MCP/YpsA-like
家族 Family family	c.129.1.1 — MoCo carrier protein-like

CATH v4.4 (6 domains)

结构域编号 domain_id	1wekA01
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	450 —

结构域编号 domain_id	1wekB01
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	450 —

结构域编号 domain_id	1wekC01
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	450 —

结构域编号 domain_id	1wekD01
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	450 —

结构域编号 domain_id	1wekE01
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	450 —

结构域编号 domain_id	1wekF01
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	450 —

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7. 引用文献 (1)

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晶胞边长 a length_a	65.650 Å
晶胞边长 b length_b	83.798 Å
晶胞边长 c length_c	265.143 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	24

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	2.200 Å
最低分辨率 resolution_low	14.940 Å
R 因子 r_factor	0.1980
R_work r_work	0.1980
R_free r_free	0.2500

fit	/app/data/saxs_computation/we/1wek/1wek.fit
pddf	/app/data/pr_computation/we/1wek/1wek.pr.out
profile	/app/data/saxs_computation/we/1wek/1wek.dat

Crystal structure of the conserved hypothetical protein TT1465 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