1w5z

AGAO covalent complex with Benzylhydrazine

Method: X-RAY DIFFRACTION Dmax: 89.7 Å Quality: REASONABLE

1. 蛋白身份与相关结构 Protein Identity & Related Structures

PHENYLETHYLAMINE OXIDASE

ARTHROBACTER GLOBIFORMIS

UniProt P46881

当前结构中的状态

Assembly 聚集状态 构建体 突变与修饰 配体、离子与共同组分 实验方法与环境 结构质量
1 蛋白同源多聚体 同源多聚体 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 A; UniProt 3–638 非标准单体:是(mmCIF未提供具体位点) CU COPPER (II) ION × 2 NA SODIUM ION × 2 SO4 SULFATE ION × 6 GOL GLYCEROL × 10 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;AGAO CRYSTALS WERE GROWN IN ABOUT 2 WEEKS BY HANGING-DROP VAPOR DIFFUSION AT 293K. THE RESERVOIR WAS 1.0-1.5M (NH4)2SO4, 2MM CUSO4, 0.15M NA CITRATE, PH 6.0-7.5. THE DROPS WERE 1.5MICROL OF 11.7 MG/ML PROTEIN, 0.05M HEPES, PH 7.0, PLUS 1.5MICROL OF RESERVOIR SOLUTION. A CRYSTAL WAS CRYOPROTECTED BY GRADUAL INCREMENTAL SOAKING IN RESERVOIR SOLUTION MIXED WITH GLYCEROL. THE CONCENTRATION OF GLYCEROL WAS INCREASED FROM 0 TO 30% IN 2-3% INCREMENTS DURING 2 HOURS. FOLLOWING CRYOPROTECTION, THE CRYSTAL WAS SOAKED FOR 15 MINUTES IN CRYOPROTECTANT WITH THE ADDITION OF 2 MILLIMOLAR BENZYLHYDRAZINE DIHYDROCHLORIDE (SIGMA). THE CRYSTAL WAS THEN FROZEN IN THE CRYOSTREAM. 分辨率 1.86 Å R-free 0.187

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly, “相对当前条目”直接指出证据层面的不同;没有差异标签表示当前已读取字段一致。

共 105 个其他 PDB 条目、143 个 assembly。 打开独立比较页并筛选聚集状态

查看构建体与数据证据
UniProt名称 PAOX_ARTGO
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–636; UniProt 3–638

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。 链映射与序列区间收在“数据证据”中;数据库内部编号、导入时间和 assembly 操作表达式仅用于维护,因此不在读者页面展示。

SAXS 散射曲线 SAXS Profile

SAXS profile for 1w5z

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1w5z
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id1w5z
沉积日期 deposition_date2004-08-11
结构标题 titleAGAO covalent complex with Benzylhydrazine
关键词 keywords;AMINE OXIDASE, ARTHROBACTER GLOBIFORMIS, COPPER CONTAINING, METAL-BINDING, OXIDOREDUCTASE, TPQ, QUINONE, INHIBITED, BH, BENZYLHYDRAZINE, 3TY ;; OXIDOREDUCTASE
实验方法 methodX-RAY DIFFRACTION

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier27.15
回转半径 Rg (电子) rg_electron25.91
零角强度 I(0) i082902500.00
分子量 molecular_weight69747.0 kDa
排除体积 excluded_volume86567 ų
包络体积 envelope_volume108630 ų
水化壳体积 shell_volume34135 ų
包络直径 envelope_diameter94.5
壳层 Rg shell_rg33.92
包络 Rg envelope_rg26.62
形状 Rg shape_rg25.88
总 Rg total_rg26.85
总原子数 total_atoms9419
残基数 n_residues620
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

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax89.7
Rg (实空间) rg_real27.06
Rg 误差 (实空间) rg_real_error0.55
I(0) (实空间) i0_real8.2900e+07
I(0) 误差 (实空间) i0_real_error1.1640e+06
Rg (倒空间) rg_reciprocal27.09
I(0) (倒空间) i0_reciprocal82900000.0000
解质量估计 total_estimate0.6843
解质量评级 solution_quality REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary32.5
偏度 Skewness skewness0.284
峰度 Kurtosis kurtosis-0.300
角度范围 angular_range— – 0.2900 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha15020000.0000
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: 0.845; Stabil: 1.000; Sysdev: 0.127; Positv: 1.000; Valcen: 0.999; Smooth: 0.976

5. 晶体学与实验 5. Crystallography & Experiment

6. 实体与聚合物信息 Entities & Polymers (6)

7. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

结构域编号 domain_idd1w5za1
类 Class classb — All beta proteins
折叠类型 Fold foldb.30 — Supersandwich
超家族 Superfamily superfamilyb.30.2 — Amine oxidase catalytic domain
家族 Family familyb.30.2.1 — Amine oxidase catalytic domain
结构域编号 domain_idd1w5za2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.17 — Cystatin-like
超家族 Superfamily superfamilyd.17.2 — Amine oxidase N-terminal region
家族 Family familyd.17.2.1 — Amine oxidase N-terminal region
结构域编号 domain_idd1w5za3
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.17 — Cystatin-like
超家族 Superfamily superfamilyd.17.2 — Amine oxidase N-terminal region
家族 Family familyd.17.2.1 — Amine oxidase N-terminal region

CATH v4.4 (3 domains)

结构域编号 domain_id1w5zA01
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily40
结构域编号 domain_id1w5zA02
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily40
结构域编号 domain_id1w5zA03
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily20 — Copper amine oxidase, catalytic domain

8. 引用文献 (1)

9. 文件与曲线 (10)