SAXSdb — 1xey

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1xey
沉积日期 deposition_date	2004-09-13
结构标题 title	Crystal structure of the complex of Escherichia coli GADA with glutarate at 2.05 A resolution
关键词 keywords	LYASE, GLUTAMATE DECARBOXYLASE, COMPLEX WITH GLUTARATE; LYASE
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	29.54 Å
回转半径 Rg (电子) rg_electron	28.60 Å
零角强度 I(0) i0	165106000.00
分子量 molecular_weight	101770.0 kDa
排除体积 excluded_volume	127050 Å³
包络体积 envelope_volume	154790 Å³
水化壳体积 shell_volume	43364 Å³
包络直径 envelope_diameter	98.9 Å
壳层 Rg shell_rg	37.34 Å
包络 Rg envelope_rg	29.06 Å
形状 Rg shape_rg	28.60 Å
总 Rg total_rg	29.37 Å
总原子数 total_atoms	7163
残基数 n_residues	897
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	96.0 Å
Rg (实空间) rg_real	29.41 Å
Rg 误差 (实空间) rg_real_error	0.71 Å
I(0) (实空间) i0_real	1.6510e+08
I(0) 误差 (实空间) i0_real_error	2.5890e+06
Rg (倒空间) rg_reciprocal	29.47 Å
I(0) (倒空间) i0_reciprocal	165100000.0000
解质量估计 total_estimate	0.8046
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	39.1 Å
偏度 Skewness skewness	0.224
峰度 Kurtosis kurtosis	-0.355
角度范围 angular_range	— – 0.2700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	87550000.0000
实空间数据点数 n_real_points	55
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 0.988; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000

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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	Glutamate decarboxylase alpha
分子量 formula_weight	52744.0 kDa
EC 编号 ec_number	4.1.1.15
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	7612

MDQKLLTDFRSELLDSRFGAKAISTIAESKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT

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 BL21

Entity 2 non-polymer

描述 description	ACETATE ION
分子量 formula_weight	59.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	PYRIDOXAL-5'-PHOSPHATE
分子量 formula_weight	247.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	GLUTARIC ACID
分子量 formula_weight	132.1 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	390

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1xeya_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.67 — PLP-dependent transferase-like
超家族 Superfamily superfamily	c.67.1 — PLP-dependent transferases
家族 Family family	c.67.1.6 — Pyridoxal-dependent decarboxylase

结构域编号 domain_id	d1xeyb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.67 — PLP-dependent transferase-like
超家族 Superfamily superfamily	c.67.1 — PLP-dependent transferases
家族 Family family	c.67.1.6 — Pyridoxal-dependent decarboxylase

CATH v4.4 (6 domains)

结构域编号 domain_id	1xeyA01
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1xeyA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	640 — Aspartate Aminotransferase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

结构域编号 domain_id	1xeyA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1150 — Aspartate Aminotransferase, domain 1
同源超家族 H-superfamily homologous superfamily	160 —

结构域编号 domain_id	1xeyB01
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1xeyB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	640 — Aspartate Aminotransferase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

结构域编号 domain_id	1xeyB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1150 — Aspartate Aminotransferase, domain 1
同源超家族 H-superfamily homologous superfamily	160 —

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7. 引用文献 (1)

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晶胞边长 a length_a	117.100 Å
晶胞边长 b length_b	117.100 Å
晶胞边长 c length_c	196.400 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	18

空间群 space_group	H 3
空间群编号 int_tables_number	146
晶系 crystal_system	—

分辨率 resolution	2.050 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.1510
R_work r_work	0.1480
R_free r_free	0.1986

fit	/app/data/saxs_computation/xe/1xey/1xey.fit
pddf	/app/data/pr_computation/xe/1xey/1xey.pr.out
profile	/app/data/saxs_computation/xe/1xey/1xey.dat

Crystal structure of the complex of Escherichia coli GADA with glutarate at 2.05 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

衍射实验 Diffraction