SAXSdb — 2daa

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2daa
沉积日期 deposition_date	1997-10-27
结构标题 title	CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY D-CYCLOSERINE
关键词 keywords	PYRIDOXAL PHOSPHATE, PYRIDOXAMINE, TRANSAMINASE, ANTIBIOTIC, SUICIDE SUBSTRATE, CYCLOSERINE, TRANSFERASE, AMINOTRANSFERASE; PYRIDOXAL PHOSPHATE
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	26.17 Å
回转半径 Rg (电子) rg_electron	25.44 Å
零角强度 I(0) i0	66084800.00
分子量 molecular_weight	63975.0 kDa
排除体积 excluded_volume	80380 Å³
包络体积 envelope_volume	94946 Å³
水化壳体积 shell_volume	31018 Å³
包络直径 envelope_diameter	85.2 Å
壳层 Rg shell_rg	33.08 Å
包络 Rg envelope_rg	25.66 Å
形状 Rg shape_rg	25.41 Å
总 Rg total_rg	26.34 Å
总原子数 total_atoms	4508
残基数 n_residues	554
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	81.7 Å
Rg (实空间) rg_real	26.15 Å
Rg 误差 (实空间) rg_real_error	0.49 Å
I(0) (实空间) i0_real	6.6080e+07
I(0) 误差 (实空间) i0_real_error	9.1610e+05
Rg (倒空间) rg_reciprocal	26.16 Å
I(0) (倒空间) i0_reciprocal	66090000.0000
解质量估计 total_estimate	0.9006
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	28.1 Å
偏度 Skewness skewness	0.345
峰度 Kurtosis kurtosis	-0.394
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	34560000.0000
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: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; 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 (3)

Entity 1 polymer

描述 description	D-AMINO ACID AMINOTRANSFERASE
分子量 formula_weight	32311.9 kDa
EC 编号 ec_number	2.6.1.21
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	4708

GYTLWNDQIVKDEEVKIDKEDRGYQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQLLHELVEKNELNTGHIYFQVTRGTSPRAHQFPENTVKPVIIGYTKENPRPLENLEKGVKATFVEDIRWLRCDIKSLNLLGAVLAKQEAHEKGCYEAILHRNNTVTEGSSSNVFGIKDGILYTHPANNMILKGITRDVVIACANEINMPVKEIPFTTHEALKMDELFVTSTTSEITPVIEIDGKLIRDGKVGEWTRKLQKQFETKIPKPLHI

来源 Source

来源生物 organism	Bacillus sp.
NCBI 分类编号 ncbi_taxonomy_id	1409
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 2 non-polymer

描述 description	D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE
分子量 formula_weight	333.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	200

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d2daaa_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.17 — D-aminoacid aminotransferase-like PLP-dependent enzymes
超家族 Superfamily superfamily	e.17.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
家族 Family family	e.17.1.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes

结构域编号 domain_id	d2daab_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.17 — D-aminoacid aminotransferase-like PLP-dependent enzymes
超家族 Superfamily superfamily	e.17.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
家族 Family family	e.17.1.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes

CATH v4.4 (4 domains)

结构域编号 domain_id	2daaA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain

结构域编号 domain_id	2daaA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	10 — D-amino Acid Aminotransferase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-amino Acid Aminotransferase, subunit A, domain 2

结构域编号 domain_id	2daaB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain

结构域编号 domain_id	2daaB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	10 — D-amino Acid Aminotransferase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-amino Acid Aminotransferase, subunit A, domain 2

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7. 引用文献 (2)

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晶胞边长 a length_a	77.301 Å
晶胞边长 b length_b	91.018 Å
晶胞边长 c length_c	89.701 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 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2050
R_work r_work	0.2050
R_free r_free	0.2600

fit	/app/data/saxs_computation/da/2daa/2daa.fit
pddf	/app/data/pr_computation/da/2daa/2daa.pr.out
profile	/app/data/saxs_computation/da/2daa/2daa.dat

CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY D-CYCLOSERINE

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