SAXSdb — 1r43

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1r43
沉积日期 deposition_date	2003-10-03
结构标题 title	Crystal structure of beta-alanine synthase from Saccharomyces kluyveri (selenomethionine substituted protein)
关键词 keywords	alpha and beta protein, one di-zinc center per subunit, HYDROLASE; HYDROLASE
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	36.58 Å
回转半径 Rg (电子) rg_electron	36.87 Å
零角强度 I(0) i0	152813000.00
分子量 molecular_weight	96833.0 kDa
排除体积 excluded_volume	119400 Å³
包络体积 envelope_volume	152340 Å³
水化壳体积 shell_volume	36352 Å³
包络直径 envelope_diameter	130.2 Å
壳层 Rg shell_rg	40.87 Å
包络 Rg envelope_rg	36.46 Å
形状 Rg shape_rg	36.92 Å
总 Rg total_rg	36.94 Å
总原子数 total_atoms	6750
残基数 n_residues	854
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	122.6 Å
Rg (实空间) rg_real	36.97 Å
Rg 误差 (实空间) rg_real_error	1.16 Å
I(0) (实空间) i0_real	1.5280e+08
I(0) 误差 (实空间) i0_real_error	2.8680e+06
Rg (倒空间) rg_reciprocal	36.73 Å
I(0) (倒空间) i0_reciprocal	152800000.0000
解质量估计 total_estimate	0.7729
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	28.5 Å
偏度 Skewness skewness	0.478
峰度 Kurtosis kurtosis	-0.594
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	47240000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.643; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.515; Smooth: 0.601

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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 (6)

Entity 1 polymer

描述 description	beta-alanine synthase
分子量 formula_weight	51281.8 kDa
EC 编号 ec_number	3.5.1.6
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	6818

MSKDVSSTITTVSASPDGTLNLPAAAPLSIASGRLNQTILETGSQFGGVARWGQESHEFGMRRLAGTALDGAMRDWFTNECESLGCKVKVDKIGNMFAVYPGKNGGKPTATGSHLDTQPEAGKYDGILGVLAGLEVLRTFKDNNYVPNYDVCVVVWFNEEGARFARSCTGSSVWSHDLSLEEAYGLMSVGEDKPESVYDSLKNIGYIGDTPASYKENEIDAHFELHIEQGPILEDENKAIGIVTGVQAYNWQKVTVHGVGAHAGTTPWRLRKDALLMSSKMIVAASEIAQRHNGLFTCGIIDAKPYSVNIIPGEVSFTLDFRHPSDDVLATMLKEAAAEFDRLIKINDGGALSYESETLQVSPAVNFHEVCIECVSRSAFAQFKKDQVRQIWSGAGHDSCQTAPHVPTSMIFIPSKDGLSHNYYEYSSPEEIENGFKVLLQAIINYDNYRVIRGHHHHHHHHH

来源 Source

来源生物 organism	Lachancea kluyveri
NCBI 分类编号 ncbi_taxonomy_id	4934
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	4

Entity 3 non-polymer

描述 description	2,3-DIHYDROXY-1,4-DITHIOBUTANE
分子量 formula_weight	154.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
分子量 formula_weight	122.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	BETA-AMINO ISOBUTYRATE
分子量 formula_weight	102.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 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	68

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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	d1r43a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
家族 Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

结构域编号 domain_id	d1r43a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.19 — Bacterial exopeptidase dimerisation domain
家族 Family family	d.58.19.1 — Bacterial exopeptidase dimerisation domain

结构域编号 domain_id	d1r43b1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
家族 Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

结构域编号 domain_id	d1r43b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.19 — Bacterial exopeptidase dimerisation domain
家族 Family family	d.58.19.1 — Bacterial exopeptidase dimerisation domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1r43A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	1r43A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	360 —

结构域编号 domain_id	1r43B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	1r43B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	360 —

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7. 引用文献 (2)

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晶胞边长 a length_a	60.430 Å
晶胞边长 b length_b	77.630 Å
晶胞边长 c length_c	110.570 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	95.63 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	29.750 Å
R 因子 r_factor	0.2139
R_work r_work	0.2106
R_free r_free	0.2740

fit	/app/data/saxs_computation/r4/1r43/1r43.fit
pddf	/app/data/pr_computation/r4/1r43/1r43.pr.out
profile	/app/data/saxs_computation/r4/1r43/1r43.dat

Crystal structure of beta-alanine synthase from Saccharomyces kluyveri (selenomethionine substituted protein)

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution