SAXSdb — 1vlu

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1vlu
沉积日期 deposition_date	2004-08-16
结构标题 title	Crystal structure of Gamma-glutamyl phosphate reductase (yor323c) from Saccharomyces cerevisiae at 2.40 A resolution
关键词 keywords	;yor323c, GAMMA-GLUTAMYL PHOSPHATE REDUCTASE, STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, Joint Center for Structural Genomics, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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	36.08 Å
回转半径 Rg (电子) rg_electron	35.42 Å
零角强度 I(0) i0	114107000.00
分子量 molecular_weight	84660.0 kDa
排除体积 excluded_volume	105540 Å³
包络体积 envelope_volume	156520 Å³
水化壳体积 shell_volume	36999 Å³
包络直径 envelope_diameter	111.0 Å
壳层 Rg shell_rg	42.36 Å
包络 Rg envelope_rg	33.53 Å
形状 Rg shape_rg	35.44 Å
总 Rg total_rg	35.92 Å
总原子数 total_atoms	5915
残基数 n_residues	780
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	113.6 Å
Rg (实空间) rg_real	35.93 Å
Rg 误差 (实空间) rg_real_error	0.95 Å
I(0) (实空间) i0_real	1.1410e+08
I(0) 误差 (实空间) i0_real_error	1.9400e+06
Rg (倒空间) rg_reciprocal	36.02 Å
I(0) (倒空间) i0_reciprocal	114100000.0000
解质量估计 total_estimate	0.8900
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	51.6 Å
偏度 Skewness skewness	0.059
峰度 Kurtosis kurtosis	-0.552
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8257000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.947

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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	Gamma-glutamyl phosphate reductase
分子量 formula_weight	51593.2 kDa
EC 编号 ec_number	1.2.1.41
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	6039

MGSDKIHHHHHHMSSSQQIAKNARKAGNILKTISNEGRSDILYKIHDALKANAHAIEEANKIDLAVAKETGLADSLLKRLDLFKGDKFEVMLQGIKDVAELEDPVGKVKMARELDDGLTLYQVTAPVGVLLVIFESRPEVIANITALSIKSGNAAILKGGKESVNTFREMAKIVNDTIAQFQSETGVPVGSVQLIETRQDVSDLLDQDEYIDLVVPRGSNALVRKIKDTTKIPVLGHADGICSIYLDEDADLIKAKRISLDAKTNYPAGCNAMETLLINPKFSKWWEVLENLTLEGGVTIHATKDLKTAYFDKLNELGKLTEAIQCKTVDADEEQDFDKEFLSLDLAAKFVTSTESAIQHINTHSSRHTDAIVTENKANAEKFMKGVDSSGVYWNASTRFADGFRYGFGAEVGISTSKIHARGPVGLDGLVSYQYQIRGDGQVASDYLGAGGNKAFVHKDLDIKTVTL

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	124

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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	d1vlua1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.82 — ALDH-like
超家族 Superfamily superfamily	c.82.1 — ALDH-like
家族 Family family	c.82.1.1 — ALDH-like

结构域编号 domain_id	d1vlua2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1vlub1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.82 — ALDH-like
超家族 Superfamily superfamily	c.82.1 — ALDH-like
家族 Family family	c.82.1.1 — ALDH-like

结构域编号 domain_id	d1vlub2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

结构域编号 domain_id	1vluA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

结构域编号 domain_id	1vluA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

结构域编号 domain_id	1vluB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

结构域编号 domain_id	1vluB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	123.041 Å
晶胞边长 b length_b	191.081 Å
晶胞边长 c length_c	125.570 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	2.290 Å
最低分辨率 resolution_low	47.830 Å
R 因子 r_factor	0.2123
R_work r_work	0.2104
R_free r_free	0.2478

fit	/app/data/saxs_computation/vl/1vlu/1vlu.fit
pddf	/app/data/pr_computation/vl/1vlu/1vlu.pr.out
profile	/app/data/saxs_computation/vl/1vlu/1vlu.dat

Crystal structure of Gamma-glutamyl phosphate reductase (yor323c) from Saccharomyces cerevisiae at 2.40 A resolution

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution