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2d5l

Crystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis

Method: X-RAY DIFFRACTION Dmax: 82.7 Å Quality: EXCELLENT

SAXS 散射曲线 SAXS Profile

SAXS profile for 2d5l

P(r) 距离分布 P(r) Distribution

P(r) distribution for 2d5l
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1. 结构基本信息 1. Structure Basics

条目编号 entry_id2d5l
沉积日期 deposition_date2005-11-02
结构标题 titleCrystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis
关键词 keywordspeptidase family S9, serine peptidase, prolyl oligopeptidase family, HYDROLASE; HYDROLASE
实验方法 methodX-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_guinier27.23 Å
回转半径 Rg (电子) rg_electron26.13 Å
零角强度 I(0) i089997500.00
分子量 molecular_weight74816.0 kDa
排除体积 excluded_volume93627 ų
包络体积 envelope_volume115780 ų
水化壳体积 shell_volume35925 ų
包络直径 envelope_diameter87.4 Å
壳层 Rg shell_rg34.50 Å
包络 Rg envelope_rg25.74 Å
形状 Rg shape_rg26.08 Å
总 Rg total_rg27.15 Å
总原子数 total_atoms5285
残基数 n_residues665
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 Å−1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3
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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax82.7 Å
Rg (实空间) rg_real27.03 Å
Rg 误差 (实空间) rg_real_error0.46 Å
I(0) (实空间) i0_real9.0000e+07
I(0) 误差 (实空间) i0_real_error1.2350e+06
Rg (倒空间) rg_reciprocal27.10 Å
I(0) (倒空间) i0_reciprocal90000000.0000
解质量估计 total_estimate0.9067
解质量评级 solution_quality EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary37.1 Å
偏度 Skewness skewness0.084
峰度 Kurtosis kurtosis-0.519
角度范围 angular_range— – 0.2900 Å−1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha19660000.0000
实空间数据点数 n_real_points59
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.984
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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)

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6. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

结构域编号 domain_id2d5lA01
类 Class class2 — Mainly Beta
架构 Architecture architecture140 — 8 Propeller
拓扑 Topology topology10 — Methanol Dehydrogenase; Chain A
同源超家族 H-superfamily homologous superfamily30 — Dipeptidylpeptidase IV, N-terminal domain
结构域编号 domain_id2d5lA02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
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7. 引用文献 (1)

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8. 文件与曲线 (10)