SAXSdb — 1p5d

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1p5d
沉积日期 deposition_date	2003-04-25
结构标题 title	Enzyme-ligand complex of P. aeruginosa PMM/PGM
关键词 keywords	ALPHA/BETA PROTEIN, PHOSPHOHEXOMUTASE, PHOSPHOSERINE, ENZYME-LIGAND COMPLEX, ENZYME-METAL COMPLEX, ISOMERASE; ISOMERASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	22.62 Å
回转半径 Rg (电子) rg_electron	21.58 Å
零角强度 I(0) i0	40271900.00
分子量 molecular_weight	49161.0 kDa
排除体积 excluded_volume	61504 Å³
包络体积 envelope_volume	69013 Å³
水化壳体积 shell_volume	26123 Å³
包络直径 envelope_diameter	72.0 Å
壳层 Rg shell_rg	28.91 Å
包络 Rg envelope_rg	21.74 Å
形状 Rg shape_rg	21.59 Å
总 Rg total_rg	22.38 Å
总原子数 total_atoms	3453
残基数 n_residues	454
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	68.4 Å
Rg (实空间) rg_real	22.50 Å
Rg 误差 (实空间) rg_real_error	0.31 Å
I(0) (实空间) i0_real	4.0270e+07
I(0) 误差 (实空间) i0_real_error	4.9170e+05
Rg (倒空间) rg_reciprocal	22.53 Å
I(0) (倒空间) i0_reciprocal	40270000.0000
解质量估计 total_estimate	0.9100
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	28.0 Å
偏度 Skewness skewness	0.176
峰度 Kurtosis kurtosis	-0.514
角度范围 angular_range	— – 0.3500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7745000.0000
实空间数据点数 n_real_points	67
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.976

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	Phosphomannomutase
分子量 formula_weight	50430.3 kDa
EC 编号 ec_number	5.4.2.8
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	X
原子数 atom_count	4026

MSTAKAPTLPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGETLANEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGVAGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHVFSAFPSDISTPEINITVTEDSKFAIIEALQRDAQWGEGNITTLDGVRVDYPKGWGLVRASNTTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF

来源 Source

来源生物 organism	Pseudomonas aeruginosa
NCBI 分类编号 ncbi_taxonomy_id	287
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	1-O-phosphono-alpha-D-glucopyranose
分子量 formula_weight	260.1 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 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	464

▼

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1p5dx1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.84 — Phosphoglucomutase, first 3 domains
超家族 Superfamily superfamily	c.84.1 — Phosphoglucomutase, first 3 domains
家族 Family family	c.84.1.1 — Phosphoglucomutase, first 3 domains

结构域编号 domain_id	d1p5dx2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.84 — Phosphoglucomutase, first 3 domains
超家族 Superfamily superfamily	c.84.1 — Phosphoglucomutase, first 3 domains
家族 Family family	c.84.1.1 — Phosphoglucomutase, first 3 domains

结构域编号 domain_id	d1p5dx3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.84 — Phosphoglucomutase, first 3 domains
超家族 Superfamily superfamily	c.84.1 — Phosphoglucomutase, first 3 domains
家族 Family family	c.84.1.1 — Phosphoglucomutase, first 3 domains

结构域编号 domain_id	d1p5dx4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.129 — TBP-like
超家族 Superfamily superfamily	d.129.2 — Phosphoglucomutase, C-terminal domain
家族 Family family	d.129.2.1 — Phosphoglucomutase, C-terminal domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1p5dX01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1p5dX02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1p5dX03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1p5dX04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	310 — TATA-Binding Protein
同源超家族 H-superfamily homologous superfamily	50 — Alpha-D-phosphohexomutase, C-terminal domain

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	70.700 Å
晶胞边长 b length_b	74.193 Å
晶胞边长 c length_c	84.836 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	4

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	1.600 Å
最低分辨率 resolution_low	25.000 Å
R 因子 r_factor	0.1568
R_work r_work	0.1557
R_free r_free	0.1790

fit	/app/data/saxs_computation/p5/1p5d/1p5d.fit
pddf	/app/data/pr_computation/p5/1p5d/1p5d.pr.out
profile	/app/data/saxs_computation/p5/1p5d/1p5d.dat

Enzyme-ligand complex of P. aeruginosa PMM/PGM

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