2cg8

The bifunctional dihydroneopterin aldolase 6-hydroxymethyl-7,8- dihydropterin synthase from Streptococcus pneumoniae

Method: X-RAY DIFFRACTION D_max: 147.1 Å Quality: REASONABLE

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	2cg8
沉积日期 deposition_date	2006-02-28
结构标题 title	The bifunctional dihydroneopterin aldolase 6-hydroxymethyl-7,8- dihydropterin synthase from Streptococcus pneumoniae
关键词 keywords	;LYASE/TRANSFERASE, ALDOLASE, FOLATE BIOSYNTHESIS, PYROPHOSPHOKINASE, LYASE, MULTIFUNCTIONAL ENZYME, TRANSFERASE, LYASE-TRANSFERASE complex ;; LYASE/TRANSFERASE
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	41.84 Å
回转半径 Rg (电子) rg_electron	41.93 Å
零角强度 I(0) i0	174672000.00
分子量 molecular_weight	112900.0 kDa
排除体积 excluded_volume	143430 Å³
包络体积 envelope_volume	194920 Å³
水化壳体积 shell_volume	41603 Å³
包络直径 envelope_diameter	144.1 Å
壳层 Rg shell_rg	43.21 Å
包络 Rg envelope_rg	41.72 Å
形状 Rg shape_rg	41.93 Å
总 Rg total_rg	42.00 Å
总原子数 total_atoms	7968
残基数 n_residues	986
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	147.1 Å
Rg (实空间) rg_real	42.19 Å
Rg 误差 (实空间) rg_real_error	1.43 Å
I(0) (实空间) i0_real	1.7470e+08
I(0) 误差 (实空间) i0_real_error	3.3580e+06
Rg (倒空间) rg_reciprocal	41.84 Å
I(0) (倒空间) i0_reciprocal	174600000.0000
解质量估计 total_estimate	0.5403
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	42.6 Å
偏度 Skewness skewness	0.510
峰度 Kurtosis kurtosis	-0.455
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	12000000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.727; Stabil: 1.000; Sysdev: 0.008; Positv: 1.000; Valcen: 0.813; Smooth: 0.000

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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) 8 domains

CATH v4.4 (8 domains)

结构域编号 domain_id	2cg8A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1130 — GTP Cyclohydrolase I, domain 2
同源超家族 H-superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

结构域编号 domain_id	2cg8A02
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	560 — 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK

结构域编号 domain_id	2cg8B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1130 — GTP Cyclohydrolase I, domain 2
同源超家族 H-superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

结构域编号 domain_id	2cg8B02
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	560 — 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK

结构域编号 domain_id	2cg8C01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1130 — GTP Cyclohydrolase I, domain 2
同源超家族 H-superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

结构域编号 domain_id	2cg8C02
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	560 — 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK

结构域编号 domain_id	2cg8D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1130 — GTP Cyclohydrolase I, domain 2
同源超家族 H-superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

结构域编号 domain_id	2cg8D02
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	560 — 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK

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7. 引用文献 (1)

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晶胞边长 a length_a	149.440 Å
晶胞边长 b length_b	149.440 Å
晶胞边长 c length_c	238.740 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	32

空间群 space_group	P 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	127.000 Å
R 因子 r_factor	0.2160
R_work r_work	0.2150
R_free r_free	0.2410

描述 description	DIHYDRONEOPTERIN ALDOLASE 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN SYNTHASE
分子量 formula_weight	31132.7 kDa
EC 编号 ec_number	4.1.2.25, 2.7.6.3
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	7968

The bifunctional dihydroneopterin aldolase 6-hydroxymethyl-7,8- dihydropterin synthase from Streptococcus pneumoniae

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) 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	STREPTOCOCCUS PNEUMONIAE
NCBI 分类编号 ncbi_taxonomy_id	1313
宿主生物 host_organism	ESCHERICHIA COLI

fit	/app/data/saxs_computation/cg/2cg8/2cg8.fit
pddf	/app/data/pr_computation/cg/2cg8/2cg8.pr.out
profile	/app/data/saxs_computation/cg/2cg8/2cg8.dat