1qmi

;Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology ;

Method: X-RAY DIFFRACTION D_max: 117.5 Å Quality: EXCELLENT

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1qmi
沉积日期 deposition_date	1999-09-28
结构标题 title	;Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology ;
关键词 keywords	;LIGASE, 2'3'CYCLIC PHOSPHATE RNA ;; 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	37.24 Å
回转半径 Rg (电子) rg_electron	36.46 Å
零角强度 I(0) i0	311791000.00
分子量 molecular_weight	142350.0 kDa
排除体积 excluded_volume	178000 Å³
包络体积 envelope_volume	229370 Å³
水化壳体积 shell_volume	51876 Å³
包络直径 envelope_diameter	119.5 Å
壳层 Rg shell_rg	43.32 Å
包络 Rg envelope_rg	35.56 Å
形状 Rg shape_rg	36.47 Å
总 Rg total_rg	36.88 Å
总原子数 total_atoms	9972
残基数 n_residues	1324
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	117.5 Å
Rg (实空间) rg_real	37.14 Å
Rg 误差 (实空间) rg_real_error	0.68 Å
I(0) (实空间) i0_real	3.1180e+08
I(0) 误差 (实空间) i0_real_error	4.6850e+06
Rg (倒空间) rg_reciprocal	37.21 Å
I(0) (倒空间) i0_reciprocal	311800000.0000
解质量估计 total_estimate	0.9018
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	42.0 Å
偏度 Skewness skewness	0.207
峰度 Kurtosis kurtosis	-0.577
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	46670000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.869

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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 (1)

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1qmia1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.2 — RNA 3'-terminal phosphate cyclase, RPTC, insert domain
家族 Family family	c.47.2.1 — RNA 3'-terminal phosphate cyclase, RPTC, insert domain

结构域编号 domain_id	d1qmia2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.1 — RNA 3'-terminal phosphate cyclase, RPTC

结构域编号 domain_id	d1qmib1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.2 — RNA 3'-terminal phosphate cyclase, RPTC, insert domain
家族 Family family	c.47.2.1 — RNA 3'-terminal phosphate cyclase, RPTC, insert domain

结构域编号 domain_id	d1qmib2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.1 — RNA 3'-terminal phosphate cyclase, RPTC

结构域编号 domain_id	d1qmic1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.2 — RNA 3'-terminal phosphate cyclase, RPTC, insert domain
家族 Family family	c.47.2.1 — RNA 3'-terminal phosphate cyclase, RPTC, insert domain

结构域编号 domain_id	d1qmic2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.1 — RNA 3'-terminal phosphate cyclase, RPTC

结构域编号 domain_id	d1qmid1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.2 — RNA 3'-terminal phosphate cyclase, RPTC, insert domain
家族 Family family	c.47.2.1 — RNA 3'-terminal phosphate cyclase, RPTC, insert domain

结构域编号 domain_id	d1qmid2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.1 — RNA 3'-terminal phosphate cyclase, RPTC

CATH v4.4 (8 domains)

结构域编号 domain_id	1qmiA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	20 — RNA 3'-terminal phosphate cyclase domain

结构域编号 domain_id	1qmiA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	20 — RNA 3'-terminal phosphate cyclase, insert domain

结构域编号 domain_id	1qmiB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	20 — RNA 3'-terminal phosphate cyclase domain

结构域编号 domain_id	1qmiB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	20 — RNA 3'-terminal phosphate cyclase, insert domain

结构域编号 domain_id	1qmiC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	20 — RNA 3'-terminal phosphate cyclase domain

结构域编号 domain_id	1qmiC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	20 — RNA 3'-terminal phosphate cyclase, insert domain

结构域编号 domain_id	1qmiD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	20 — RNA 3'-terminal phosphate cyclase domain

结构域编号 domain_id	1qmiD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	20 — RNA 3'-terminal phosphate cyclase, insert domain

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7. 引用文献 (1)

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晶胞边长 a length_a	101.800 Å
晶胞边长 b length_b	126.600 Å
晶胞边长 c length_c	128.800 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	16

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	2.800 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.2440
R_work r_work	0.2440
R_free r_free	0.3310

描述 description	;RNA 3'-TERMINAL PHOSPHATE CYCLASE ;
分子量 formula_weight	37248.7 kDa
EC 编号 ec_number	6.5.1.4
来源方法 src_method	man
拷贝数 entity_count	4

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	9972

;Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology ;

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 (1)

Entity 1 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	ESCHERICHIA COLI
NCBI 分类编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	ESCHERICHIA COLI

fit	/app/data/saxs_computation/qm/1qmi/1qmi.fit
pddf	/app/data/pr_computation/qm/1qmi/1qmi.pr.out
profile	/app/data/saxs_computation/qm/1qmi/1qmi.dat