SAXSdb — 1gll

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1gll
沉积日期 deposition_date	1998-09-24
结构标题 title	ESCHERICHIA COLI GLYCEROL KINASE MUTANT WITH BOUND ATP ANALOG SHOWING SUBSTANTIAL DOMAIN MOTION
关键词 keywords	PHOSPHOTRANSFERASE, KINASE, DOMAIN MOTION, ALLOSTERIC REGULATION; PHOSPHOTRANSFERASE
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	34.85 Å
回转半径 Rg (电子) rg_electron	34.70 Å
零角强度 I(0) i0	199904000.00
分子量 molecular_weight	112290.0 kDa
排除体积 excluded_volume	139670 Å³
包络体积 envelope_volume	163540 Å³
水化壳体积 shell_volume	40733 Å³
包络直径 envelope_diameter	117.3 Å
壳层 Rg shell_rg	39.86 Å
包络 Rg envelope_rg	34.64 Å
形状 Rg shape_rg	34.69 Å
总 Rg total_rg	35.06 Å
总原子数 total_atoms	7896
残基数 n_residues	988
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	114.5 Å
Rg (实空间) rg_real	35.05 Å
Rg 误差 (实空间) rg_real_error	0.80 Å
I(0) (实空间) i0_real	1.9990e+08
I(0) 误差 (实空间) i0_real_error	2.9880e+06
Rg (倒空间) rg_reciprocal	34.93 Å
I(0) (倒空间) i0_reciprocal	199900000.0000
解质量估计 total_estimate	0.8417
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	30.5 Å
偏度 Skewness skewness	0.452
峰度 Kurtosis kurtosis	-0.578
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	120500000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.776; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.878; Smooth: 0.731

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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	GLYCEROL KINASE
分子量 formula_weight	56261.5 kDa
EC 编号 ec_number	2.7.1.30
突变 mutation	S58W
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	Y,O
原子数 atom_count	7896

TEKKYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSWTLVEVLAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGLEDYIRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHVTDYTNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIGGKGGTRIPISGIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNYALEGAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPYARGAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQFQSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERNYRYAGWKKAVKRAMAWEEHDE

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	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
分子量 formula_weight	505.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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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	d1gllo1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.4 — Glycerol kinase

结构域编号 domain_id	d1gllo2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.4 — Glycerol kinase

结构域编号 domain_id	d1glly1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.4 — Glycerol kinase

结构域编号 domain_id	d1glly2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.4 — Glycerol kinase

CATH v4.4 (4 domains)

结构域编号 domain_id	1gllO01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	1gllO02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	1gllY01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	1gllY02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

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7. 引用文献 (1)

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晶胞边长 a length_a	99.766 Å
晶胞边长 b length_b	201.148 Å
晶胞边长 c length_c	114.340 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	16

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.1760
R_free r_free	—

fit	/app/data/saxs_computation/gl/1gll/1gll.fit
pddf	/app/data/pr_computation/gl/1gll/1gll.pr.out
profile	/app/data/saxs_computation/gl/1gll/1gll.dat

ESCHERICHIA COLI GLYCEROL KINASE MUTANT WITH BOUND ATP ANALOG SHOWING SUBSTANTIAL DOMAIN MOTION

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