SAXSdb — 1v8f

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1v8f
沉积日期 deposition_date	2004-01-08
结构标题 title	Crystal Structure of Pantoate-beta-Alanine (Pantothenate Synthetase) from Thermus Thermophilus HB8
关键词 keywords	Ligase, Rossmann Fold, Dimer, Structural Genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI; 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	28.14 Å
回转半径 Rg (电子) rg_electron	27.30 Å
零角强度 I(0) i0	62122400.00
分子量 molecular_weight	62705.0 kDa
排除体积 excluded_volume	79031 Å³
包络体积 envelope_volume	94550 Å³
水化壳体积 shell_volume	29774 Å³
包络直径 envelope_diameter	94.6 Å
壳层 Rg shell_rg	33.68 Å
包络 Rg envelope_rg	27.38 Å
形状 Rg shape_rg	27.30 Å
总 Rg total_rg	27.96 Å
总原子数 total_atoms	4420
残基数 n_residues	552
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	91.3 Å
Rg (实空间) rg_real	28.22 Å
Rg 误差 (实空间) rg_real_error	0.64 Å
I(0) (实空间) i0_real	6.2120e+07
I(0) 误差 (实空间) i0_real_error	8.9240e+05
Rg (倒空间) rg_reciprocal	28.20 Å
I(0) (倒空间) i0_reciprocal	62120000.0000
解质量估计 total_estimate	0.8854
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	29.4 Å
偏度 Skewness skewness	0.395
峰度 Kurtosis kurtosis	-0.452
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15770000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.886

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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 (6)

Entity 1 polymer

描述 description	Pantoate-beta-alanine ligase
分子量 formula_weight	30733.3 kDa
EC 编号 ec_number	6.3.2.1
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	5144

MRTVSTVAELRAALPREGVGFVPTMGYLHRGHLALVERARRENPFVVVSVFVNPLQFGPGEDYHRYPRDLERDRALLQEAGVDLLFAPGVEEMYPEGFATRVQVEGPLTALWEGAVRPGHFQGVATVVARLFLLVQPQRAYFGEKDYQQLLVVRRMVRDLGFPVEVVGVPTVREEDGLALSSRNVYLSPETRKKAPVLYRALLAMREVAGQGGSVAEALRAGEEALRAVPEFRKDYLAIVHPETLLPLSDWVAGARGIVAGRFPEARLIDNLEVYP

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

Entity 2 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 3 non-polymer

描述 description	TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
分子量 formula_weight	122.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	HEXAETHYLENE GLYCOL
分子量 formula_weight	282.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 6 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	724

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1v8fa_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
家族 Family family	c.26.1.4 — Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)

结构域编号 domain_id	d1v8fb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
家族 Family family	c.26.1.4 — Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)

CATH v4.4 (4 domains)

结构域编号 domain_id	1v8fA01
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	620 — HUPs

结构域编号 domain_id	1v8fA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1300 — Pantoate--beta-alanine Ligase; Chain: A,domain 2
同源超家族 H-superfamily homologous superfamily	10 — Pantoate-beta-alanine ligase, C-terminal domain

结构域编号 domain_id	1v8fB01
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	620 — HUPs

结构域编号 domain_id	1v8fB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1300 — Pantoate--beta-alanine Ligase; Chain: A,domain 2
同源超家族 H-superfamily homologous superfamily	10 — Pantoate-beta-alanine ligase, C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	88.514 Å
晶胞边长 b length_b	88.514 Å
晶胞边长 c length_c	266.720 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 61 2 2
空间群编号 int_tables_number	178
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	—
R_work r_work	0.2050
R_free r_free	0.2570

fit	/app/data/saxs_computation/v8/1v8f/1v8f.fit
pddf	/app/data/pr_computation/v8/1v8f/1v8f.pr.out
profile	/app/data/saxs_computation/v8/1v8f/1v8f.dat

Crystal Structure of Pantoate-beta-Alanine (Pantothenate Synthetase) from Thermus Thermophilus HB8

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution