1wpg
Crystal structure of the SR CA2+-ATPase with MGF4
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 | 1wpg |
| 沉积日期 deposition_date | 2004-09-02 |
| 结构标题 title | Crystal structure of the SR CA2+-ATPase with MGF4 |
| 关键词 keywords | MEMBRANE PROTEIN, P-TYPE ATPASE, HAD FOLD, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR |
| 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 | 67.04 Å |
| 回转半径 Rg (电子) rg_electron | 66.19 Å |
| 零角强度 I(0) i0 | 2672380000.00 |
| 分子量 molecular_weight | 442850.0 kDa |
| 排除体积 excluded_volume | 557230 ų |
| 包络体积 envelope_volume | 890040 ų |
| 水化壳体积 shell_volume | 114290 ų |
| 包络直径 envelope_diameter | 216.3 Å |
| 壳层 Rg shell_rg | 65.66 Å |
| 包络 Rg envelope_rg | 63.19 Å |
| 形状 Rg shape_rg | 66.16 Å |
| 总 Rg total_rg | 66.28 Å |
| 总原子数 total_atoms | 31008 |
| 残基数 n_residues | 3976 |
| 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 | 217.3 Å |
| Rg (实空间) rg_real | 66.96 Å |
| Rg 误差 (实空间) rg_real_error | 1.87 Å |
| I(0) (实空间) i0_real | 2.6720e+09 |
| I(0) 误差 (实空间) i0_real_error | 5.9850e+07 |
| Rg (倒空间) rg_reciprocal | 67.20 Å |
| I(0) (倒空间) i0_reciprocal | 2673000000.0000 |
| 解质量估计 total_estimate | 0.8561 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 94.5 Å |
| 偏度 Skewness skewness | 0.143 |
| 峰度 Kurtosis kurtosis | -0.566 |
| 角度范围 angular_range | — – 0.1150 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 88300000.0000 |
| 实空间数据点数 n_real_points | 24 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.303 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (7)
6. 折叠分类 (SCOP + CATH) 32 domains
SCOP 2.08 (16 domains)
| 结构域编号 domain_id | d1wpga1 |
| 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.82.7 — Metal cation-transporting ATPase, actuator domain A |
| 家族 Family family | b.82.7.1 — Metal cation-transporting ATPase, actuator domain A |
| 结构域编号 domain_id | d1wpga2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.108 — HAD-like |
| 超家族 Superfamily superfamily | c.108.1 — HAD-like |
| 家族 Family family | c.108.1.7 — Meta-cation ATPase, catalytic domain P |
| 结构域编号 domain_id | d1wpga3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.220 — Metal cation-transporting ATPase, ATP-binding domain N |
| 超家族 Superfamily superfamily | d.220.1 — Metal cation-transporting ATPase, ATP-binding domain N |
| 家族 Family family | d.220.1.1 — Metal cation-transporting ATPase, ATP-binding domain N |
| 结构域编号 domain_id | d1wpga4 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.33 — Metal cation-transporting ATPase, transmembrane domain |
| 超家族 Superfamily superfamily | f.33.1 — Metal cation-transporting ATPase, transmembrane domain |
| 家族 Family family | f.33.1.1 — Metal cation-transporting ATPase, transmembrane domain |
| 结构域编号 domain_id | d1wpgb1 |
| 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.82.7 — Metal cation-transporting ATPase, actuator domain A |
| 家族 Family family | b.82.7.1 — Metal cation-transporting ATPase, actuator domain A |
| 结构域编号 domain_id | d1wpgb2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.108 — HAD-like |
| 超家族 Superfamily superfamily | c.108.1 — HAD-like |
| 家族 Family family | c.108.1.7 — Meta-cation ATPase, catalytic domain P |
| 结构域编号 domain_id | d1wpgb3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.220 — Metal cation-transporting ATPase, ATP-binding domain N |
| 超家族 Superfamily superfamily | d.220.1 — Metal cation-transporting ATPase, ATP-binding domain N |
| 家族 Family family | d.220.1.1 — Metal cation-transporting ATPase, ATP-binding domain N |
| 结构域编号 domain_id | d1wpgb4 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.33 — Metal cation-transporting ATPase, transmembrane domain |
| 超家族 Superfamily superfamily | f.33.1 — Metal cation-transporting ATPase, transmembrane domain |
| 家族 Family family | f.33.1.1 — Metal cation-transporting ATPase, transmembrane domain |
| 结构域编号 domain_id | d1wpgc1 |
| 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.82.7 — Metal cation-transporting ATPase, actuator domain A |
| 家族 Family family | b.82.7.1 — Metal cation-transporting ATPase, actuator domain A |
| 结构域编号 domain_id | d1wpgc2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.108 — HAD-like |
| 超家族 Superfamily superfamily | c.108.1 — HAD-like |
| 家族 Family family | c.108.1.7 — Meta-cation ATPase, catalytic domain P |
| 结构域编号 domain_id | d1wpgc3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.220 — Metal cation-transporting ATPase, ATP-binding domain N |
| 超家族 Superfamily superfamily | d.220.1 — Metal cation-transporting ATPase, ATP-binding domain N |
| 家族 Family family | d.220.1.1 — Metal cation-transporting ATPase, ATP-binding domain N |
| 结构域编号 domain_id | d1wpgc4 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.33 — Metal cation-transporting ATPase, transmembrane domain |
| 超家族 Superfamily superfamily | f.33.1 — Metal cation-transporting ATPase, transmembrane domain |
| 家族 Family family | f.33.1.1 — Metal cation-transporting ATPase, transmembrane domain |
| 结构域编号 domain_id | d1wpgd1 |
| 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.82.7 — Metal cation-transporting ATPase, actuator domain A |
| 家族 Family family | b.82.7.1 — Metal cation-transporting ATPase, actuator domain A |
| 结构域编号 domain_id | d1wpgd2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.108 — HAD-like |
| 超家族 Superfamily superfamily | c.108.1 — HAD-like |
| 家族 Family family | c.108.1.7 — Meta-cation ATPase, catalytic domain P |
| 结构域编号 domain_id | d1wpgd3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.220 — Metal cation-transporting ATPase, ATP-binding domain N |
| 超家族 Superfamily superfamily | d.220.1 — Metal cation-transporting ATPase, ATP-binding domain N |
| 家族 Family family | d.220.1.1 — Metal cation-transporting ATPase, ATP-binding domain N |
| 结构域编号 domain_id | d1wpgd4 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.33 — Metal cation-transporting ATPase, transmembrane domain |
| 超家族 Superfamily superfamily | f.33.1 — Metal cation-transporting ATPase, transmembrane domain |
| 家族 Family family | f.33.1.1 — Metal cation-transporting ATPase, transmembrane domain |
CATH v4.4 (16 domains)
| 结构域编号 domain_id | 1wpgA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 70 — Distorted Sandwich |
| 拓扑 Topology topology | 150 — Calcium-transporting ATPase, cytoplasmic transduction domain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Calcium-transporting ATPase, cytoplasmic transduction domain A |
| 结构域编号 domain_id | 1wpgA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1110 — Calcium-transporting ATPase, transmembrane domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — Calcium-transporting ATPase, transmembrane domain |
| 结构域编号 domain_id | 1wpgA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1110 — Calcium-transporting ATPase, cytoplasmic domain N |
| 同源超家族 H-superfamily homologous superfamily | 10 — Calcium-transporting ATPase, cytoplasmic domain N |
| 结构域编号 domain_id | 1wpgA04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 1000 — HAD superfamily/HAD-like |
| 结构域编号 domain_id | 1wpgB01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 70 — Distorted Sandwich |
| 拓扑 Topology topology | 150 — Calcium-transporting ATPase, cytoplasmic transduction domain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Calcium-transporting ATPase, cytoplasmic transduction domain A |
| 结构域编号 domain_id | 1wpgB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1110 — Calcium-transporting ATPase, transmembrane domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — Calcium-transporting ATPase, transmembrane domain |
| 结构域编号 domain_id | 1wpgB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1110 — Calcium-transporting ATPase, cytoplasmic domain N |
| 同源超家族 H-superfamily homologous superfamily | 10 — Calcium-transporting ATPase, cytoplasmic domain N |
| 结构域编号 domain_id | 1wpgB04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 1000 — HAD superfamily/HAD-like |
| 结构域编号 domain_id | 1wpgC01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 70 — Distorted Sandwich |
| 拓扑 Topology topology | 150 — Calcium-transporting ATPase, cytoplasmic transduction domain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Calcium-transporting ATPase, cytoplasmic transduction domain A |
| 结构域编号 domain_id | 1wpgC02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1110 — Calcium-transporting ATPase, transmembrane domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — Calcium-transporting ATPase, transmembrane domain |
| 结构域编号 domain_id | 1wpgC03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1110 — Calcium-transporting ATPase, cytoplasmic domain N |
| 同源超家族 H-superfamily homologous superfamily | 10 — Calcium-transporting ATPase, cytoplasmic domain N |
| 结构域编号 domain_id | 1wpgC04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 1000 — HAD superfamily/HAD-like |
| 结构域编号 domain_id | 1wpgD01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 70 — Distorted Sandwich |
| 拓扑 Topology topology | 150 — Calcium-transporting ATPase, cytoplasmic transduction domain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Calcium-transporting ATPase, cytoplasmic transduction domain A |
| 结构域编号 domain_id | 1wpgD02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1110 — Calcium-transporting ATPase, transmembrane domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — Calcium-transporting ATPase, transmembrane domain |
| 结构域编号 domain_id | 1wpgD03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1110 — Calcium-transporting ATPase, cytoplasmic domain N |
| 同源超家族 H-superfamily homologous superfamily | 10 — Calcium-transporting ATPase, cytoplasmic domain N |
| 结构域编号 domain_id | 1wpgD04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 1000 — HAD superfamily/HAD-like |