SAXSdb — 1v1b

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1v1b
沉积日期 deposition_date	2004-04-13
结构标题 title	2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND ATP
关键词 keywords	;2-KETO-3-DEOXYGLUCONATE KINASE, ATP, THERMUS THERMOPHILUS, STRUCTURAL GENOMICS, TRANSFERASE, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI ;; 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	50.54 Å
回转半径 Rg (电子) rg_electron	51.03 Å
零角强度 I(0) i0	253192000.00
分子量 molecular_weight	131400.0 kDa
排除体积 excluded_volume	164380 Å³
包络体积 envelope_volume	228710 Å³
水化壳体积 shell_volume	39875 Å³
包络直径 envelope_diameter	171.0 Å
壳层 Rg shell_rg	49.44 Å
包络 Rg envelope_rg	49.94 Å
形状 Rg shape_rg	51.03 Å
总 Rg total_rg	50.98 Å
总原子数 total_atoms	9280
残基数 n_residues	1204
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	163.8 Å
Rg (实空间) rg_real	51.01 Å
Rg 误差 (实空间) rg_real_error	1.88 Å
I(0) (实空间) i0_real	2.5320e+08
I(0) 误差 (实空间) i0_real_error	4.6540e+06
Rg (倒空间) rg_reciprocal	50.12 Å
I(0) (倒空间) i0_reciprocal	252900000.0000
解质量估计 total_estimate	0.6641
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	26.4 Å
偏度 Skewness skewness	0.420
峰度 Kurtosis kurtosis	-0.826
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8916000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.430; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.265; Smooth: 0.075

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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	2-KETO-3-DEOXYGLUCONATE KINASE
分子量 formula_weight	33470.2 kDa
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	9373

MLEVVTAGEPLVALVPQEPGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAPGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLWSPEEARGFLERALPGVDLLFLSEEEAELLFGRVEEALRALSAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLANLLGASVAASRGDHEGAPYREDLEVLLKATQTFMR

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

Entity 2 non-polymer

描述 description	ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	93

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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	d1v1ba_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.72 — Ribokinase-like
超家族 Superfamily superfamily	c.72.1 — Ribokinase-like
家族 Family family	c.72.1.1 — Ribokinase-like

结构域编号 domain_id	d1v1bb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.72 — Ribokinase-like
超家族 Superfamily superfamily	c.72.1 — Ribokinase-like
家族 Family family	c.72.1.1 — Ribokinase-like

结构域编号 domain_id	d1v1bc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.72 — Ribokinase-like
超家族 Superfamily superfamily	c.72.1 — Ribokinase-like
家族 Family family	c.72.1.1 — Ribokinase-like

结构域编号 domain_id	d1v1bd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.72 — Ribokinase-like
超家族 Superfamily superfamily	c.72.1 — Ribokinase-like
家族 Family family	c.72.1.1 — Ribokinase-like

CATH v4.4 (4 domains)

结构域编号 domain_id	1v1bA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
同源超家族 H-superfamily homologous superfamily	20 — Ribokinase

结构域编号 domain_id	1v1bB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
同源超家族 H-superfamily homologous superfamily	20 — Ribokinase

结构域编号 domain_id	1v1bC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
同源超家族 H-superfamily homologous superfamily	20 — Ribokinase

结构域编号 domain_id	1v1bD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
同源超家族 H-superfamily homologous superfamily	20 — Ribokinase

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7. 引用文献 (2)

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晶胞边长 a length_a	84.721 Å
晶胞边长 b length_b	84.721 Å
晶胞边长 c length_c	321.613 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	120.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	P 63
空间群编号 int_tables_number	173
晶系 crystal_system	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	29.460 Å
R 因子 r_factor	0.1779
R_work r_work	0.1779
R_free r_free	0.2658

fit	/app/data/saxs_computation/v1/1v1b/1v1b.fit
pddf	/app/data/pr_computation/v1/1v1b/1v1b.pr.out
profile	/app/data/saxs_computation/v1/1v1b/1v1b.dat

2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND ATP

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