1vlo

;Crystal structure of aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system (np417381) from Escherichia coli k12 at 1.70 A resolution ;

Method: X-RAY DIFFRACTION D_max: 70.7 Å Quality: GOOD

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	1vlo
沉积日期 deposition_date	2004-08-05
结构标题 title	;Crystal structure of aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system (np417381) from Escherichia coli k12 at 1.70 A resolution ;
关键词 keywords	;np417381, aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system, STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, Joint Center for Structural Genomics, TRANSFERASE ;; 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	21.92 Å
回转半径 Rg (电子) rg_electron	20.88 Å
零角强度 I(0) i0	29240800.00
分子量 molecular_weight	40420.0 kDa
排除体积 excluded_volume	49889 Å³
包络体积 envelope_volume	57644 Å³
水化壳体积 shell_volume	22874 Å³
包络直径 envelope_diameter	72.4 Å
壳层 Rg shell_rg	27.60 Å
包络 Rg envelope_rg	21.10 Å
形状 Rg shape_rg	20.92 Å
总 Rg total_rg	21.58 Å
总原子数 total_atoms	2800
残基数 n_residues	351
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	70.7 Å
Rg (实空间) rg_real	21.82 Å
Rg 误差 (实空间) rg_real_error	0.43 Å
I(0) (实空间) i0_real	2.9240e+07
I(0) 误差 (实空间) i0_real_error	4.0480e+05
Rg (倒空间) rg_reciprocal	21.84 Å
I(0) (倒空间) i0_reciprocal	29240000.0000
解质量估计 total_estimate	0.8972
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	26.4 Å
偏度 Skewness skewness	0.222
峰度 Kurtosis kurtosis	-0.430
角度范围 angular_range	— – 0.3600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	5319000.0000
实空间数据点数 n_real_points	68
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.977

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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 (2)

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6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1vloa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.44 — Elongation factor/aminomethyltransferase common domain
超家族 Superfamily superfamily	b.44.2 — Aminomethyltransferase beta-barrel domain
家族 Family family	b.44.2.1 — Aminomethyltransferase beta-barrel domain

结构域编号 domain_id	d1vloa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.250 — Folate-binding domain
超家族 Superfamily superfamily	d.250.1 — Folate-binding domain
家族 Family family	d.250.1.1 — Aminomethyltransferase folate-binding domain

结构域编号 domain_id	d1vloa3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

结构域编号 domain_id	1vloA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	120 — Probable tRNA modification gtpase trme; domain 1

结构域编号 domain_id	1vloA02
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	1400 — Aminomethyltransferase beta-barrel domains

结构域编号 domain_id	1vloA03
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	1250 — Aminomethyltransferase fragment
同源超家族 H-superfamily homologous superfamily	10 — Aminomethyltransferase fragment

结构域编号 domain_id	1vloA04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	110 — Aminomethyltransferase beta-barrel domains

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7. 引用文献 (1)

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晶胞边长 a length_a	46.517 Å
晶胞边长 b length_b	64.564 Å
晶胞边长 c length_c	117.141 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	1.700 Å
最低分辨率 resolution_low	43.380 Å
R 因子 r_factor	0.1605
R_work r_work	0.1587
R_free r_free	0.1951

描述 description	Aminomethyltransferase
分子量 formula_weight	42711.3 kDa
EC 编号 ec_number	2.1.2.10
突变 mutation	2.1.2.10
来源方法 src_method	man
拷贝数 entity_count	1

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	3253

;Crystal structure of aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system (np417381) from Escherichia coli k12 at 1.70 A resolution ;

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

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 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 K12
NCBI 分类编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	419

fit	/app/data/saxs_computation/vl/1vlo/1vlo.fit
pddf	/app/data/pr_computation/vl/1vlo/1vlo.pr.out
profile	/app/data/saxs_computation/vl/1vlo/1vlo.dat