SAXSdb — 1n2h

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1n2h
沉积日期 deposition_date	2002-10-22
结构标题 title	Crystal Structure of a Pantothenate Synthetase from M. tuberculosis in complex with a reaction intermediate, pantoyl adenylate
关键词 keywords	;Structural genomics, Rossmann fold, dimer, intersubunit beta sheet, PSI, Protein Structure Initiative, TB Structural Genomics Consortium, TBSGC, 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	27.88 Å
回转半径 Rg (电子) rg_electron	26.97 Å
零角强度 I(0) i0	62309300.00
分子量 molecular_weight	61755.0 kDa
排除体积 excluded_volume	77448 Å³
包络体积 envelope_volume	93231 Å³
水化壳体积 shell_volume	29588 Å³
包络直径 envelope_diameter	91.4 Å
壳层 Rg shell_rg	33.58 Å
包络 Rg envelope_rg	27.06 Å
形状 Rg shape_rg	26.98 Å
总 Rg total_rg	27.60 Å
总原子数 total_atoms	4338
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	89.0 Å
Rg (实空间) rg_real	27.92 Å
Rg 误差 (实空间) rg_real_error	0.53 Å
I(0) (实空间) i0_real	6.2310e+07
I(0) 误差 (实空间) i0_real_error	9.1410e+05
Rg (倒空间) rg_reciprocal	27.91 Å
I(0) (倒空间) i0_reciprocal	62310000.0000
解质量估计 total_estimate	0.8921
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	28.1 Å
偏度 Skewness skewness	0.343
峰度 Kurtosis kurtosis	-0.504
角度范围 angular_range	— – 0.2850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	17990000.0000
实空间数据点数 n_real_points	58
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.844

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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 (7)

Entity 1 polymer

描述 description	pantothenate synthetase
分子量 formula_weight	31500.1 kDa
EC 编号 ec_number	6.3.2.1
突变 mutation	T2A, E77G
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	4637

MAIPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGGDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGTFAGTDRPDGYR

来源 Source

来源生物 organism	Mycobacterium tuberculosis
NCBI 分类编号 ncbi_taxonomy_id	1773
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	PANTOYL ADENYLATE
分子量 formula_weight	477.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	1

Entity 6 non-polymer

描述 description	ETHANOL
分子量 formula_weight	46.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 7 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	299

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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	d1n2ha_
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	d1n2hb_
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	1n2hA01
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	1n2hA02
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	1n2hB01
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	1n2hB02
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	48.258 Å
晶胞边长 b length_b	70.861 Å
晶胞边长 c length_c	81.822 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	99.34 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	19.820 Å
R 因子 r_factor	0.1820
R_work r_work	0.1820
R_free r_free	0.2180

fit	/app/data/saxs_computation/n2/1n2h/1n2h.fit
pddf	/app/data/pr_computation/n2/1n2h/1n2h.pr.out
profile	/app/data/saxs_computation/n2/1n2h/1n2h.dat

Crystal Structure of a Pantothenate Synthetase from M. tuberculosis in complex with a reaction intermediate, pantoyl adenylate

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution