SAXSdb — 1jkx

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1jkx
沉积日期 deposition_date	2001-07-13
结构标题 title	Unexpected formation of an epoxide-derived multisubstrate adduct inhibitor on the active site of GAR transformylase
关键词 keywords	PURINE BIOSYNTHESIS, ANTI-CANCER AGENT, ENZYME-ASSEMBLED MULTISUBSTRATE ADDUCT INHIBITOR 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	36.12 Å
回转半径 Rg (电子) rg_electron	35.42 Å
零角强度 I(0) i0	142525000.00
分子量 molecular_weight	94607.0 kDa
排除体积 excluded_volume	117840 Å³
包络体积 envelope_volume	160040 Å³
水化壳体积 shell_volume	38971 Å³
包络直径 envelope_diameter	116.8 Å
壳层 Rg shell_rg	40.72 Å
包络 Rg envelope_rg	34.55 Å
形状 Rg shape_rg	35.43 Å
总 Rg total_rg	35.74 Å
总原子数 total_atoms	6676
残基数 n_residues	836
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	114.8 Å
Rg (实空间) rg_real	36.00 Å
Rg 误差 (实空间) rg_real_error	1.02 Å
I(0) (实空间) i0_real	1.4250e+08
I(0) 误差 (实空间) i0_real_error	2.4240e+06
Rg (倒空间) rg_reciprocal	36.08 Å
I(0) (倒空间) i0_reciprocal	142500000.0000
解质量估计 total_estimate	0.8986
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	52.2 Å
偏度 Skewness skewness	0.079
峰度 Kurtosis kurtosis	-0.676
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	18070000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.940

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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	PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
分子量 formula_weight	23266.3 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	7283

MNIVVLISGNGSNLQAIIDACKTNKIKGTVRAVFSNKADAFGLERARQAGIATHTLIASAFDSREAYDRELIHEIDMYAPDVVVLAGFMRILSPAFVSHYAGRLLNIHPSLLPKYPGLHTHRQALENGDEEHGTSVHFVTDELDGGPVILQAKVPVFAGDSEDDITARVQTQEHAIYPLVISWFADGRLKMHENAAWLDGQRLPPQGYAADE

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	;N-[5'-O-PHOSPHONO-RIBOFURANOSYL]-2-[2-HYDROXY-2-[4-[GLUTAMIC ACID]-N-CARBONYLPHENYL]-3-[2-AMINO-4-HYDROXY-QUINAZOLIN-6-YL]-PROPANYLAMINO]-ACETAMIDE ;
分子量 formula_weight	752.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	607

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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	d1jkxa_
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	d1jkxb_
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	d1jkxc_
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	d1jkxd_
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	1jkxA00
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	1jkxB00
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	1jkxC00
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	1jkxD00
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 (2)

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晶胞边长 a length_a	55.140 Å
晶胞边长 b length_b	56.010 Å
晶胞边长 c length_c	76.130 Å
晶胞夹角 α angle_alpha	80.83 °
晶胞夹角 β angle_beta	71.71 °
晶胞夹角 γ angle_gamma	83.69 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	1.600 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2210
R_work r_work	0.2210
R_free r_free	0.2430

fit	/app/data/saxs_computation/jk/1jkx/1jkx.fit
pddf	/app/data/pr_computation/jk/1jkx/1jkx.pr.out
profile	/app/data/saxs_computation/jk/1jkx/1jkx.dat

Unexpected formation of an epoxide-derived multisubstrate adduct inhibitor on the active site of GAR transformylase

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