2gre

Crystal structure of Deblocking aminopeptidase from Bacillus cereus

Method: X-RAY DIFFRACTION Dmax: 208.3 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

SAXS profile for 2gre

P(r) 距离分布 P(r) Distribution

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

条目编号 entry_id2gre
沉积日期 deposition_date2006-04-24
结构标题 titleCrystal structure of Deblocking aminopeptidase from Bacillus cereus
关键词 keywords;Bacillus cereus Deblocking aminopeptidase, Structural Genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, HYDROLASE ;; HYDROLASE
实验方法 methodX-RAY DIFFRACTION

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier65.15
回转半径 Rg (电子) rg_electron65.64
零角强度 I(0) i04404860000.00
分子量 molecular_weight552440.0 kDa
排除体积 excluded_volume687020 ų
包络体积 envelope_volume1062100 ų
水化壳体积 shell_volume140780 ų
包络直径 envelope_diameter233.1
壳层 Rg shell_rg63.55
包络 Rg envelope_rg63.60
形状 Rg shape_rg65.66
总 Rg total_rg65.52
总原子数 total_atoms38577
残基数 n_residues4822
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −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

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax208.3
Rg (实空间) rg_real65.47
Rg 误差 (实空间) rg_real_error1.56
I(0) (实空间) i0_real4.4040e+09
I(0) 误差 (实空间) i0_real_error9.7730e+07
Rg (倒空间) rg_reciprocal64.81
I(0) (倒空间) i0_reciprocal4399000000.0000
解质量估计 total_estimate0.8124
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary78.1
偏度 Skewness skewness0.526
峰度 Kurtosis kurtosis-0.089
角度范围 angular_range— – 0.1200 −1
当前正则化参数 α current_alpha0.0007
最高正则化参数 α highest_alpha184300000.0000
实空间数据点数 n_real_points25
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.790; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.198

4. 晶体学与实验 4. Crystallography & Experiment

5. 实体与聚合体信息 (3)

6. 折叠分类 (SCOP + CATH) 64 domains

SCOP 2.08 (32 domains)

结构域编号 domain_idd2grea1
类 Class classb — All beta proteins
折叠类型 Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamilyb.49.3 — Aminopeptidase/glucanase lid domain
家族 Family familyb.49.3.1 — Aminopeptidase/glucanase lid domain
结构域编号 domain_idd2grea2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
家族 Family familyc.56.5.4 — Bacterial dinuclear zinc exopeptidases
结构域编号 domain_idd2greb1
类 Class classb — All beta proteins
折叠类型 Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamilyb.49.3 — Aminopeptidase/glucanase lid domain
家族 Family familyb.49.3.1 — Aminopeptidase/glucanase lid domain
结构域编号 domain_idd2greb2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
家族 Family familyc.56.5.4 — Bacterial dinuclear zinc exopeptidases
结构域编号 domain_idd2grec1
类 Class classb — All beta proteins
折叠类型 Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamilyb.49.3 — Aminopeptidase/glucanase lid domain
家族 Family familyb.49.3.1 — Aminopeptidase/glucanase lid domain
结构域编号 domain_idd2grec2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
家族 Family familyc.56.5.4 — Bacterial dinuclear zinc exopeptidases
结构域编号 domain_idd2gred1
类 Class classb — All beta proteins
折叠类型 Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamilyb.49.3 — Aminopeptidase/glucanase lid domain
家族 Family familyb.49.3.1 — Aminopeptidase/glucanase lid domain
结构域编号 domain_idd2gred2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
家族 Family familyc.56.5.4 — Bacterial dinuclear zinc exopeptidases
结构域编号 domain_idd2gree1
类 Class classb — All beta proteins
折叠类型 Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamilyb.49.3 — Aminopeptidase/glucanase lid domain
家族 Family familyb.49.3.1 — Aminopeptidase/glucanase lid domain
结构域编号 domain_idd2gree2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
家族 Family familyc.56.5.4 — Bacterial dinuclear zinc exopeptidases
结构域编号 domain_idd2gref1
类 Class classb — All beta proteins
折叠类型 Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamilyb.49.3 — Aminopeptidase/glucanase lid domain
家族 Family familyb.49.3.1 — Aminopeptidase/glucanase lid domain
结构域编号 domain_idd2gref2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
家族 Family familyc.56.5.4 — Bacterial dinuclear zinc exopeptidases
结构域编号 domain_idd2greg1
类 Class classb — All beta proteins
折叠类型 Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamilyb.49.3 — Aminopeptidase/glucanase lid domain
家族 Family familyb.49.3.1 — Aminopeptidase/glucanase lid domain
结构域编号 domain_idd2greg2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
家族 Family familyc.56.5.4 — Bacterial dinuclear zinc exopeptidases
结构域编号 domain_idd2greh1
类 Class classb — All beta proteins
折叠类型 Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamilyb.49.3 — Aminopeptidase/glucanase lid domain
家族 Family familyb.49.3.1 — Aminopeptidase/glucanase lid domain
结构域编号 domain_idd2greh2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
家族 Family familyc.56.5.4 — Bacterial dinuclear zinc exopeptidases
结构域编号 domain_idd2grei1
类 Class classb — All beta proteins
折叠类型 Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamilyb.49.3 — Aminopeptidase/glucanase lid domain
家族 Family familyb.49.3.1 — Aminopeptidase/glucanase lid domain
结构域编号 domain_idd2grei2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
家族 Family familyc.56.5.4 — Bacterial dinuclear zinc exopeptidases
结构域编号 domain_idd2grej1
类 Class classb — All beta proteins
折叠类型 Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamilyb.49.3 — Aminopeptidase/glucanase lid domain
家族 Family familyb.49.3.1 — Aminopeptidase/glucanase lid domain
结构域编号 domain_idd2grej2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
家族 Family familyc.56.5.4 — Bacterial dinuclear zinc exopeptidases
结构域编号 domain_idd2grek1
类 Class classb — All beta proteins
折叠类型 Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamilyb.49.3 — Aminopeptidase/glucanase lid domain
家族 Family familyb.49.3.1 — Aminopeptidase/glucanase lid domain
结构域编号 domain_idd2grek2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
家族 Family familyc.56.5.4 — Bacterial dinuclear zinc exopeptidases
结构域编号 domain_idd2grel1
类 Class classb — All beta proteins
折叠类型 Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamilyb.49.3 — Aminopeptidase/glucanase lid domain
家族 Family familyb.49.3.1 — Aminopeptidase/glucanase lid domain
结构域编号 domain_idd2grel2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
家族 Family familyc.56.5.4 — Bacterial dinuclear zinc exopeptidases
结构域编号 domain_idd2grem1
类 Class classb — All beta proteins
折叠类型 Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamilyb.49.3 — Aminopeptidase/glucanase lid domain
家族 Family familyb.49.3.1 — Aminopeptidase/glucanase lid domain
结构域编号 domain_idd2grem2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
家族 Family familyc.56.5.4 — Bacterial dinuclear zinc exopeptidases
结构域编号 domain_idd2gren1
类 Class classb — All beta proteins
折叠类型 Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamilyb.49.3 — Aminopeptidase/glucanase lid domain
家族 Family familyb.49.3.1 — Aminopeptidase/glucanase lid domain
结构域编号 domain_idd2gren2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
家族 Family familyc.56.5.4 — Bacterial dinuclear zinc exopeptidases
结构域编号 domain_idd2greo1
类 Class classb — All beta proteins
折叠类型 Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamilyb.49.3 — Aminopeptidase/glucanase lid domain
家族 Family familyb.49.3.1 — Aminopeptidase/glucanase lid domain
结构域编号 domain_idd2greo2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
家族 Family familyc.56.5.4 — Bacterial dinuclear zinc exopeptidases
结构域编号 domain_idd2grep1
类 Class classb — All beta proteins
折叠类型 Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamilyb.49.3 — Aminopeptidase/glucanase lid domain
家族 Family familyb.49.3.1 — Aminopeptidase/glucanase lid domain
结构域编号 domain_idd2grep2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
家族 Family familyc.56.5.4 — Bacterial dinuclear zinc exopeptidases

CATH v4.4 (32 domains)

结构域编号 domain_id2greA01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily10 — Zn peptidases
结构域编号 domain_id2greA02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily40 — Peptidase M42, domain 2
结构域编号 domain_id2greB01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily10 — Zn peptidases
结构域编号 domain_id2greB02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily40 — Peptidase M42, domain 2
结构域编号 domain_id2greC01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily10 — Zn peptidases
结构域编号 domain_id2greC02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily40 — Peptidase M42, domain 2
结构域编号 domain_id2greD01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily10 — Zn peptidases
结构域编号 domain_id2greD02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily40 — Peptidase M42, domain 2
结构域编号 domain_id2greE01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily10 — Zn peptidases
结构域编号 domain_id2greE02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily40 — Peptidase M42, domain 2
结构域编号 domain_id2greF01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily10 — Zn peptidases
结构域编号 domain_id2greF02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily40 — Peptidase M42, domain 2
结构域编号 domain_id2greG01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily10 — Zn peptidases
结构域编号 domain_id2greG02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily40 — Peptidase M42, domain 2
结构域编号 domain_id2greH01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily10 — Zn peptidases
结构域编号 domain_id2greH02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily40 — Peptidase M42, domain 2
结构域编号 domain_id2greI01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily10 — Zn peptidases
结构域编号 domain_id2greI02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily40 — Peptidase M42, domain 2
结构域编号 domain_id2greJ01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily10 — Zn peptidases
结构域编号 domain_id2greJ02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily40 — Peptidase M42, domain 2
结构域编号 domain_id2greK01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily10 — Zn peptidases
结构域编号 domain_id2greK02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily40 — Peptidase M42, domain 2
结构域编号 domain_id2greL01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily10 — Zn peptidases
结构域编号 domain_id2greL02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily40 — Peptidase M42, domain 2
结构域编号 domain_id2greM01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily10 — Zn peptidases
结构域编号 domain_id2greM02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily40 — Peptidase M42, domain 2
结构域编号 domain_id2greN01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily10 — Zn peptidases
结构域编号 domain_id2greN02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily40 — Peptidase M42, domain 2
结构域编号 domain_id2greO01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily10 — Zn peptidases
结构域编号 domain_id2greO02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily40 — Peptidase M42, domain 2
结构域编号 domain_id2greP01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily10 — Zn peptidases
结构域编号 domain_id2greP02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily40 — Peptidase M42, domain 2

7. 引用文献 (1)

8. 文件与曲线 (10)