SAXSdb — 1hxq

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hxq
沉积日期 deposition_date	1996-06-16
结构标题 title	THE STRUCTURE OF NUCLEOTIDYLATED GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE FROM ESCHERICHIA COLI AT 1.86 ANGSTROMS RESOLUTION
关键词 keywords	METALLOENZYME, NUCLEOTIDYLATED HISTIDINE, REACTION INTERMEDIATE, NUCLEOTIDYLTRANSFERASE; NUCLEOTIDYLTRANSFERASE
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	26.20 Å
回转半径 Rg (电子) rg_electron	25.02 Å
零角强度 I(0) i0	102187000.00
分子量 molecular_weight	77391.0 kDa
排除体积 excluded_volume	95770 Å³
包络体积 envelope_volume	111410 Å³
水化壳体积 shell_volume	35593 Å³
包络直径 envelope_diameter	78.9 Å
壳层 Rg shell_rg	33.65 Å
包络 Rg envelope_rg	25.00 Å
形状 Rg shape_rg	25.01 Å
总 Rg total_rg	25.90 Å
总原子数 total_atoms	5449
残基数 n_residues	673
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	76.0 Å
Rg (实空间) rg_real	26.02 Å
Rg 误差 (实空间) rg_real_error	0.35 Å
I(0) (实空间) i0_real	1.0220e+08
I(0) 误差 (实空间) i0_real_error	1.2660e+06
Rg (倒空间) rg_reciprocal	26.08 Å
I(0) (倒空间) i0_reciprocal	102200000.0000
解质量估计 total_estimate	0.7308
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	33.6 Å
偏度 Skewness skewness	0.092
峰度 Kurtosis kurtosis	-0.561
角度范围 angular_range	— – 0.3050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15320000.0000
实空间数据点数 n_real_points	62
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.976; Stabil: 1.000; Sysdev: 0.221; Positv: 1.000; Valcen: 0.983; Smooth: 0.925

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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 (5)

Entity 1 polymer

描述 description	HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
分子量 formula_weight	39694.6 kDa
EC 编号 ec_number	2.7.7.12
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	6179

MTQFNPVDHPHRRYNPLTGQWILVSPHRAKRPWQGAQETPAKQVLPAHDPDCFLCAGNVRVTGDKNPDYTGTYVFTNDFAALMSDTPDAPESHDPLMRCQSARGTSRVICFSPDHSKTLPELSVAALTEIVKTWQEQTAELGKTYPWVQVFENKGAAMGCSNPHPHGQIWANSFLPNEAEREDRLQKEYFAEQKSPMLVDYVQRELADGSRTVVETEHWLAVVPYWAAWPFETLLLPKAHVLRITDLTDAQRSDLALALKKLTSRYDNLFQCSFPYSMGWHGAPFNGEENQHWQLHAHFYPPLLRSATVRKFMVGYEMLAETQRDLTAEQAAERLRAVSDIHFRESGV

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	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	URIDINE-5'-MONOPHOSPHATE
分子量 formula_weight	324.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	730

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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	d1hxqa1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.13 — HIT-like
超家族 Superfamily superfamily	d.13.1 — HIT-like
家族 Family family	d.13.1.2 — Hexose-1-phosphate uridylyltransferase

结构域编号 domain_id	d1hxqa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.13 — HIT-like
超家族 Superfamily superfamily	d.13.1 — HIT-like
家族 Family family	d.13.1.2 — Hexose-1-phosphate uridylyltransferase

结构域编号 domain_id	d1hxqb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.13 — HIT-like
超家族 Superfamily superfamily	d.13.1 — HIT-like
家族 Family family	d.13.1.2 — Hexose-1-phosphate uridylyltransferase

结构域编号 domain_id	d1hxqb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.13 — HIT-like
超家族 Superfamily superfamily	d.13.1 — HIT-like
家族 Family family	d.13.1.2 — Hexose-1-phosphate uridylyltransferase

CATH v4.4 (4 domains)

结构域编号 domain_id	1hxqA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	428 — HIT family, subunit A
同源超家族 H-superfamily homologous superfamily	10 — HIT-like

结构域编号 domain_id	1hxqA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	428 — HIT family, subunit A
同源超家族 H-superfamily homologous superfamily	10 — HIT-like

结构域编号 domain_id	1hxqB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	428 — HIT family, subunit A
同源超家族 H-superfamily homologous superfamily	10 — HIT-like

结构域编号 domain_id	1hxqB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	428 — HIT family, subunit A
同源超家族 H-superfamily homologous superfamily	10 — HIT-like

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7. 引用文献 (5)

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晶胞边长 a length_a	57.200 Å
晶胞边长 b length_b	215.400 Å
晶胞边长 c length_c	68.900 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	8

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	1.860 Å
最低分辨率 resolution_low	65.000 Å
R 因子 r_factor	—
R_work r_work	0.1960
R_free r_free	—

fit	/app/data/saxs_computation/hx/1hxq/1hxq.fit
pddf	/app/data/pr_computation/hx/1hxq/1hxq.pr.out
profile	/app/data/saxs_computation/hx/1hxq/1hxq.dat

THE STRUCTURE OF NUCLEOTIDYLATED GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE FROM ESCHERICHIA COLI AT 1.86 ANGSTROMS 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

衍射实验 Diffraction