1rby

Human GAR Tfase complex structure with 10-(trifluoroacetyl)-5,10-dideazaacyclic-5,6,7,8-tetrahydrofolic acid and substrate beta-GAR

Method: X-RAY DIFFRACTION D_max: 115.3 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	1rby
沉积日期 deposition_date	2003-11-03
结构标题 title	Human GAR Tfase complex structure with 10-(trifluoroacetyl)-5,10-dideazaacyclic-5,6,7,8-tetrahydrofolic acid and substrate beta-GAR
关键词 keywords	PROTEIN-COFACTOR ANALOGUE COMPLEX, 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	34.70 Å
回转半径 Rg (电子) rg_electron	34.46 Å
零角强度 I(0) i0	120117000.00
分子量 molecular_weight	88445.0 kDa
排除体积 excluded_volume	111210 Å³
包络体积 envelope_volume	144860 Å³
水化壳体积 shell_volume	36006 Å³
包络直径 envelope_diameter	116.5 Å
壳层 Rg shell_rg	39.77 Å
包络 Rg envelope_rg	34.03 Å
形状 Rg shape_rg	34.48 Å
总 Rg total_rg	34.82 Å
总原子数 total_atoms	6216
残基数 n_residues	800
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	115.3 Å
Rg (实空间) rg_real	34.81 Å
Rg 误差 (实空间) rg_real_error	0.86 Å
I(0) (实空间) i0_real	1.2010e+08
I(0) 误差 (实空间) i0_real_error	1.9890e+06
Rg (倒空间) rg_reciprocal	34.74 Å
I(0) (倒空间) i0_reciprocal	120100000.0000
解质量估计 total_estimate	0.8857
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	32.6 Å
偏度 Skewness skewness	0.349
峰度 Kurtosis kurtosis	-0.541
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	28680000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.927; Smooth: 0.901

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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 (4)

Entity 1 polymer

描述 description	PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
分子量 formula_weight	22678.9 kDa
EC 编号 ec_number	2.1.2.2
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	6727

ARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWVKEEHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	;N-{4-[(1R)-4-[(2R,4R,5S)-2,4-DIAMINO-6-OXOHEXAHYDROPYRIMIDIN-5-YL]-1-(2,2,2-TRIFLUORO-1,1-DIHYDROXYETHYL)BUTYL]BENZOYL}-D-GLUTAMIC ACID ;
分子量 formula_weight	549.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	GLYCINAMIDE RIBONUCLEOTIDE
分子量 formula_weight	284.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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	511

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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	d1rbya_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.65 — Formyltransferase
超家族 Superfamily superfamily	c.65.1 — Formyltransferase
家族 Family family	c.65.1.1 — Formyltransferase

结构域编号 domain_id	d1rbyb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.65 — Formyltransferase
超家族 Superfamily superfamily	c.65.1 — Formyltransferase
家族 Family family	c.65.1.1 — Formyltransferase

结构域编号 domain_id	d1rbyc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.65 — Formyltransferase
超家族 Superfamily superfamily	c.65.1 — Formyltransferase
家族 Family family	c.65.1.1 — Formyltransferase

结构域编号 domain_id	d1rbyd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.65 — Formyltransferase
超家族 Superfamily superfamily	c.65.1 — Formyltransferase
家族 Family family	c.65.1.1 — Formyltransferase

CATH v4.4 (4 domains)

结构域编号 domain_id	1rbyA00
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	170 — Formyl transferase, N-terminal domain

结构域编号 domain_id	1rbyB00
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	170 — Formyl transferase, N-terminal domain

结构域编号 domain_id	1rbyC00
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	170 — Formyl transferase, N-terminal domain

结构域编号 domain_id	1rbyD00
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	170 — Formyl transferase, N-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	126.171 Å
晶胞边长 b length_b	126.171 Å
晶胞边长 c length_c	95.389 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 31
空间群编号 int_tables_number	144
晶系 crystal_system	—

分辨率 resolution	2.101 Å
最低分辨率 resolution_low	47.670 Å
R 因子 r_factor	0.2459
R_work r_work	0.2449
R_free r_free	0.2643

fit	/app/data/saxs_computation/rb/1rby/1rby.fit
pddf	/app/data/pr_computation/rb/1rby/1rby.pr.out
profile	/app/data/saxs_computation/rb/1rby/1rby.dat