SAXSdb — 1m0s

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1m0s
沉积日期 deposition_date	2002-06-14
结构标题 title	NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG ID IR21)
关键词 keywords	;D-Ribose 5-phosphate Isomerase, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, IR21, Haemophilus influenzae, structural genomics, PSI, Protein Structure Initiative, NESG, ISOMERASE ;; ISOMERASE
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	24.54 Å
回转半径 Rg (电子) rg_electron	23.92 Å
零角强度 I(0) i0	35785600.00
分子量 molecular_weight	46674.0 kDa
排除体积 excluded_volume	58817 Å³
包络体积 envelope_volume	67869 Å³
水化壳体积 shell_volume	24557 Å³
包络直径 envelope_diameter	88.9 Å
壳层 Rg shell_rg	30.31 Å
包络 Rg envelope_rg	24.06 Å
形状 Rg shape_rg	23.89 Å
总 Rg total_rg	24.78 Å
总原子数 total_atoms	3272
残基数 n_residues	438
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	85.3 Å
Rg (实空间) rg_real	24.64 Å
Rg 误差 (实空间) rg_real_error	0.65 Å
I(0) (实空间) i0_real	3.5790e+07
I(0) 误差 (实空间) i0_real_error	4.9840e+05
Rg (倒空间) rg_reciprocal	24.62 Å
I(0) (倒空间) i0_reciprocal	35790000.0000
解质量估计 total_estimate	0.8533
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	25.7 Å
偏度 Skewness skewness	0.485
峰度 Kurtosis kurtosis	-0.204
角度范围 angular_range	— – 0.3250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	14400000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.747; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.851; Smooth: 0.997

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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	Ribose-5-Phosphate Isomerase A
分子量 formula_weight	23172.7 kDa
EC 编号 ec_number	5.3.1.6
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	3604

MNQLEMKKLAAQAALQYVKADRIVGVGSGSTVNCFIEALGTIKDKIQGAVAASKESEELLRKQGIEVFNANDVSSLDIYVDGADEINPQKMMIKGGGAALTREKIVAALAKKFICIVDSSKQVDVLGSTFPLPVEVIPMARSQVGRKLAALGGSPEYREGVVTDNGNVILDVHNFSILNPVEIEKELNNVAGVVTNGIFALRGADVVIVGTPEGAKVID

来源 Source

来源生物 organism	Haemophilus influenzae
NCBI 分类编号 ncbi_taxonomy_id	727
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	CITRIC ACID
分子量 formula_weight	192.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	332

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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	d1m0sa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.124 — NagB/RpiA/CoA transferase-like
超家族 Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
家族 Family family	c.124.1.4 — D-ribose-5-phosphate isomerase (RpiA), catalytic domain

结构域编号 domain_id	d1m0sa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.40 — D-ribose-5-phosphate isomerase (RpiA), lid domain
家族 Family family	d.58.40.1 — D-ribose-5-phosphate isomerase (RpiA), lid domain

结构域编号 domain_id	d1m0sb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.124 — NagB/RpiA/CoA transferase-like
超家族 Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
家族 Family family	c.124.1.4 — D-ribose-5-phosphate isomerase (RpiA), catalytic domain

结构域编号 domain_id	d1m0sb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.40 — D-ribose-5-phosphate isomerase (RpiA), lid domain
家族 Family family	d.58.40.1 — D-ribose-5-phosphate isomerase (RpiA), lid domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1m0sA01
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	1360 —

结构域编号 domain_id	1m0sA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	260 — ACT domain

结构域编号 domain_id	1m0sB01
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	1360 —

结构域编号 domain_id	1m0sB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	260 — ACT domain

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7. 引用文献 (1)

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晶胞边长 a length_a	42.826 Å
晶胞边长 b length_b	96.737 Å
晶胞边长 c length_c	122.050 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	8

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	1.900 Å
最低分辨率 resolution_low	25.810 Å
R 因子 r_factor	0.1790
R_work r_work	0.1790
R_free r_free	0.2080

fit	/app/data/saxs_computation/m0/1m0s/1m0s.fit
pddf	/app/data/pr_computation/m0/1m0s/1m0s.pr.out
profile	/app/data/saxs_computation/m0/1m0s/1m0s.dat

NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG ID IR21)

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