SAXSdb — 1usl

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1usl
沉积日期 deposition_date	2003-11-25
结构标题 title	Structure Of Mycobacterium tuberculosis Ribose-5-Phosphate Isomerase, RpiB, Rv2465c, Complexed With Phosphate.
关键词 keywords	;ISOMERASE, PHOSPHOPENTOSE ISOMERASE B, PENTOSE PHOSPHATE PATHWAY, RV2465C, PHOSPHORIBOISOMERASE B, STRUCTURAL PROTEOMICS IN EUROPE, SPINE, STRUCTURAL GENOMICS ;; 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	30.50 Å
回转半径 Rg (电子) rg_electron	29.85 Å
零角强度 I(0) i0	126306000.00
分子量 molecular_weight	84479.0 kDa
排除体积 excluded_volume	103970 Å³
包络体积 envelope_volume	130950 Å³
水化壳体积 shell_volume	36845 Å³
包络直径 envelope_diameter	104.7 Å
壳层 Rg shell_rg	36.53 Å
包络 Rg envelope_rg	30.10 Å
形状 Rg shape_rg	29.84 Å
总 Rg total_rg	30.45 Å
总原子数 total_atoms	5940
残基数 n_residues	788
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	99.1 Å
Rg (实空间) rg_real	30.46 Å
Rg 误差 (实空间) rg_real_error	0.66 Å
I(0) (实空间) i0_real	1.2630e+08
I(0) 误差 (实空间) i0_real_error	1.8360e+06
Rg (倒空间) rg_reciprocal	30.48 Å
I(0) (倒空间) i0_reciprocal	126300000.0000
解质量估计 total_estimate	0.9000
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	34.3 Å
偏度 Skewness skewness	0.255
峰度 Kurtosis kurtosis	-0.498
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	43570000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.963

▶

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

▶

5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	RIBOSE 5-PHOSPHATE ISOMERASE B
分子量 formula_weight	18330.7 kDa
EC 编号 ec_number	5.3.1.6
来源方法 src_method	man
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E
原子数 atom_count	6519

MAHHHHHHMSGMRVYLGADHAGYELKQRIIEHLKQTGHEPIDCGALRYDADDDYPAFCIAAATRTVADPGSLGIVLGGSGNGEQIAANKVPGARCALAWSVQTAALAREHNNAQLIGIGGRMHTVAEALAIVDAFVTTPWSKAQRHQRRIDILAEYERTHEAPPVPGAPA

来源 Source

来源生物 organism	MYCOBACTERIUM TUBERCULOSIS
NCBI 分类编号 ncbi_taxonomy_id	83332
宿主生物 host_organism	ESCHERICHIA COLI

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	5

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	579

▼

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d1usla_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.121 — Ribose/Galactose isomerase RpiB/AlsB
超家族 Superfamily superfamily	c.121.1 — Ribose/Galactose isomerase RpiB/AlsB
家族 Family family	c.121.1.1 — Ribose/Galactose isomerase RpiB/AlsB

结构域编号 domain_id	d1uslb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.121 — Ribose/Galactose isomerase RpiB/AlsB
超家族 Superfamily superfamily	c.121.1 — Ribose/Galactose isomerase RpiB/AlsB
家族 Family family	c.121.1.1 — Ribose/Galactose isomerase RpiB/AlsB

结构域编号 domain_id	d1uslc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.121 — Ribose/Galactose isomerase RpiB/AlsB
超家族 Superfamily superfamily	c.121.1 — Ribose/Galactose isomerase RpiB/AlsB
家族 Family family	c.121.1.1 — Ribose/Galactose isomerase RpiB/AlsB

结构域编号 domain_id	d1usld_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.121 — Ribose/Galactose isomerase RpiB/AlsB
超家族 Superfamily superfamily	c.121.1 — Ribose/Galactose isomerase RpiB/AlsB
家族 Family family	c.121.1.1 — Ribose/Galactose isomerase RpiB/AlsB

结构域编号 domain_id	d1usle_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.121 — Ribose/Galactose isomerase RpiB/AlsB
超家族 Superfamily superfamily	c.121.1 — Ribose/Galactose isomerase RpiB/AlsB
家族 Family family	c.121.1.1 — Ribose/Galactose isomerase RpiB/AlsB

CATH v4.4 (5 domains)

结构域编号 domain_id	1uslA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

结构域编号 domain_id	1uslB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

结构域编号 domain_id	1uslC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

结构域编号 domain_id	1uslD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

结构域编号 domain_id	1uslE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	136.420 Å
晶胞边长 b length_b	102.390 Å
晶胞边长 c length_c	69.610 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	95.68 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	20

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.880 Å
最低分辨率 resolution_low	81.650 Å
R 因子 r_factor	0.1702
R_work r_work	0.1685
R_free r_free	0.2018

fit	/app/data/saxs_computation/us/1usl/1usl.fit
pddf	/app/data/pr_computation/us/1usl/1usl.pr.out
profile	/app/data/saxs_computation/us/1usl/1usl.dat

Structure Of Mycobacterium tuberculosis Ribose-5-Phosphate Isomerase, RpiB, Rv2465c, Complexed With Phosphate.

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

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

Entity 3 water

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)