1l6j
Crystal structure of human matrix metalloproteinase MMP9 (gelatinase B).
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 | 1l6j |
| 沉积日期 deposition_date | 2002-03-11 |
| 结构标题 title | Crystal structure of human matrix metalloproteinase MMP9 (gelatinase B). |
| 关键词 keywords | Twisted beta sheet flanked by helices, HYDROLASE; HYDROLASE |
| 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 | 24.57 Å |
| 回转半径 Rg (电子) rg_electron | 23.79 Å |
| 零角强度 I(0) i0 | 36494400.00 |
| 分子量 molecular_weight | 45256.0 kDa |
| 排除体积 excluded_volume | 55848 ų |
| 包络体积 envelope_volume | 67581 ų |
| 水化壳体积 shell_volume | 24258 ų |
| 包络直径 envelope_diameter | 81.5 Å |
| 壳层 Rg shell_rg | 30.19 Å |
| 包络 Rg envelope_rg | 23.65 Å |
| 形状 Rg shape_rg | 23.81 Å |
| 总 Rg total_rg | 24.48 Å |
| 总原子数 total_atoms | 3185 |
| 残基数 n_residues | 405 |
| 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 | 78.2 Å |
| Rg (实空间) rg_real | 24.51 Å |
| Rg 误差 (实空间) rg_real_error | 0.47 Å |
| I(0) (实空间) i0_real | 3.6490e+07 |
| I(0) 误差 (实空间) i0_real_error | 5.5990e+05 |
| Rg (倒空间) rg_reciprocal | 24.53 Å |
| I(0) (倒空间) i0_reciprocal | 36490000.0000 |
| 解质量估计 total_estimate | 0.9089 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 29.8 Å |
| 偏度 Skewness skewness | 0.243 |
| 峰度 Kurtosis kurtosis | -0.477 |
| 角度范围 angular_range | — – 0.3250 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 5487000.0000 |
| 实空间数据点数 n_real_points | 64 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.996 |
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) 10 domains
SCOP 2.08 (5 domains)
| 结构域编号 domain_id | d1l6ja1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.20 — PGBD-like |
| 超家族 Superfamily superfamily | a.20.1 — PGBD-like |
| 家族 Family family | a.20.1.2 — MMP N-terminal domain |
| 结构域编号 domain_id | d1l6ja2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.92 — Zincin-like |
| 超家族 Superfamily superfamily | d.92.1 — Metalloproteases ('zincins'), catalytic domain |
| 家族 Family family | d.92.1.11 — Matrix metalloproteases, catalytic domain |
| 结构域编号 domain_id | d1l6ja3 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.14 — Kringle-like |
| 超家族 Superfamily superfamily | g.14.1 — Kringle-like |
| 家族 Family family | g.14.1.2 — Fibronectin type II module |
| 结构域编号 domain_id | d1l6ja4 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.14 — Kringle-like |
| 超家族 Superfamily superfamily | g.14.1 — Kringle-like |
| 家族 Family family | g.14.1.2 — Fibronectin type II module |
| 结构域编号 domain_id | d1l6ja5 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.14 — Kringle-like |
| 超家族 Superfamily superfamily | g.14.1 — Kringle-like |
| 家族 Family family | g.14.1.2 — Fibronectin type II module |
CATH v4.4 (5 domains)
| 结构域编号 domain_id | 1l6jA01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 101 — Muramoyl-pentapeptide Carboxypeptidase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — PGBD-like superfamily/PGBD |
| 结构域编号 domain_id | 1l6jA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 390 — Collagenase (Catalytic Domain) |
| 同源超家族 H-superfamily homologous superfamily | 10 — Collagenase (Catalytic Domain) |
| 结构域编号 domain_id | 1l6jA03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 10 — Ribbon |
| 拓扑 Topology topology | 10 — Seminal Fluid Protein PDC-109 (Domain B) |
| 同源超家族 H-superfamily homologous superfamily | 10 — Fibronectin, type II, collagen-binding |
| 结构域编号 domain_id | 1l6jA04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 10 — Ribbon |
| 拓扑 Topology topology | 10 — Seminal Fluid Protein PDC-109 (Domain B) |
| 同源超家族 H-superfamily homologous superfamily | 10 — Fibronectin, type II, collagen-binding |
| 结构域编号 domain_id | 1l6jA05 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 10 — Ribbon |
| 拓扑 Topology topology | 10 — Seminal Fluid Protein PDC-109 (Domain B) |
| 同源超家族 H-superfamily homologous superfamily | 10 — Fibronectin, type II, collagen-binding |