1zz9
Crystal Structure of FeII HppE
SAXS 散射曲线 SAXS Profile
P(r) 距离分布 P(r) Distribution
1. 结构基本信息 1. Structure Basics
| 条目编号 entry_id | 1zz9 |
| 沉积日期 deposition_date | 2005-06-13 |
| 结构标题 title | Crystal Structure of FeII HppE |
| 关键词 keywords | Mononuclear iron enzyme, Cupin, holo-HppE, OXIDOREDUCTASE; OXIDOREDUCTASE |
| 实验方法 method | X-RAY DIFFRACTION |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 33.36 Å |
| 回转半径 Rg (电子) rg_electron | 32.92 Å |
| 零角强度 I(0) i0 | 61941400.00 |
| 分子量 molecular_weight | 61400.0 kDa |
| 排除体积 excluded_volume | 76618 ų |
| 包络体积 envelope_volume | 108850 ų |
| 水化壳体积 shell_volume | 29635 ų |
| 包络直径 envelope_diameter | 105.2 Å |
| 壳层 Rg shell_rg | 37.01 Å |
| 包络 Rg envelope_rg | 31.96 Å |
| 形状 Rg shape_rg | 32.93 Å |
| 总 Rg total_rg | 33.26 Å |
| 总原子数 total_atoms | 4315 |
| 残基数 n_residues | 575 |
| 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/ų |
| 壳层衬度 contrast_shell | 0.0300 e/ų |
| CRYSOL 版本 crysol_version | 4.1.3 |
3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)
| 最大尺寸 Dmax dmax | 102.8 Å |
| Rg (实空间) rg_real | 33.32 Å |
| Rg 误差 (实空间) rg_real_error | 0.61 Å |
| I(0) (实空间) i0_real | 6.1940e+07 |
| I(0) 误差 (实空间) i0_real_error | 9.3750e+05 |
| Rg (倒空间) rg_reciprocal | 33.35 Å |
| I(0) (倒空间) i0_reciprocal | 61940000.0000 |
| 解质量估计 total_estimate | 0.7170 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 45.9 Å |
| 偏度 Skewness skewness | 0.138 |
| 峰度 Kurtosis kurtosis | -0.724 |
| 角度范围 angular_range | — – 0.2350 Å−1 |
| 当前正则化参数 α current_alpha | 0.0001 |
| 最高正则化参数 α highest_alpha | 5172000.0000 |
| 实空间数据点数 n_real_points | 48 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.979; Stabil: 1.000; Sysdev: 0.214; Positv: 1.000; Valcen: 0.957; Smooth: 0.779 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1zz9a1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.35 — lambda repressor-like DNA-binding domains |
| 超家族 Superfamily superfamily | a.35.1 — lambda repressor-like DNA-binding domains |
| 家族 Family family | a.35.1.3 — SinR domain-like |
| 结构域编号 domain_id | d1zz9a2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.82 — Double-stranded beta-helix |
| 超家族 Superfamily superfamily | b.82.1 — RmlC-like cupins |
| 家族 Family family | b.82.1.10 — TM1459-like |
| 结构域编号 domain_id | d1zz9b1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.35 — lambda repressor-like DNA-binding domains |
| 超家族 Superfamily superfamily | a.35.1 — lambda repressor-like DNA-binding domains |
| 家族 Family family | a.35.1.3 — SinR domain-like |
| 结构域编号 domain_id | d1zz9b2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.82 — Double-stranded beta-helix |
| 超家族 Superfamily superfamily | b.82.1 — RmlC-like cupins |
| 家族 Family family | b.82.1.10 — TM1459-like |
| 结构域编号 domain_id | d1zz9c1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.35 — lambda repressor-like DNA-binding domains |
| 超家族 Superfamily superfamily | a.35.1 — lambda repressor-like DNA-binding domains |
| 家族 Family family | a.35.1.3 — SinR domain-like |
| 结构域编号 domain_id | d1zz9c2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.82 — Double-stranded beta-helix |
| 超家族 Superfamily superfamily | b.82.1 — RmlC-like cupins |
| 家族 Family family | b.82.1.10 — TM1459-like |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1zz9A01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 260 — 434 Repressor (Amino-terminal Domain) |
| 同源超家族 H-superfamily homologous superfamily | 40 — lambda repressor-like DNA-binding domains |
| 结构域编号 domain_id | 1zz9A02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 10 — Jelly Rolls |
| 结构域编号 domain_id | 1zz9B01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 260 — 434 Repressor (Amino-terminal Domain) |
| 同源超家族 H-superfamily homologous superfamily | 40 — lambda repressor-like DNA-binding domains |
| 结构域编号 domain_id | 1zz9B02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 10 — Jelly Rolls |
| 结构域编号 domain_id | 1zz9C01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 260 — 434 Repressor (Amino-terminal Domain) |
| 同源超家族 H-superfamily homologous superfamily | 40 — lambda repressor-like DNA-binding domains |
| 结构域编号 domain_id | 1zz9C02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 10 — Jelly Rolls |