1s4d
Crystal Structure Analysis of the S-adenosyl-L-methionine dependent uroporphyrinogen-III C-methyltransferase SUMT
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 | 1s4d |
| 沉积日期 deposition_date | 2004-01-16 |
| 结构标题 title | Crystal Structure Analysis of the S-adenosyl-L-methionine dependent uroporphyrinogen-III C-methyltransferase SUMT |
| 关键词 keywords | tetrapyrrole biosynthesis, cobalamin, SAM, SAH, uroporphyrinogen-III methyltransferase, Transferase; TRANSFERASE |
| 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 | 58.74 Å |
| 回转半径 Rg (电子) rg_electron | 58.60 Å |
| 零角强度 I(0) i0 | 1483330000.00 |
| 分子量 molecular_weight | 324750.0 kDa |
| 排除体积 excluded_volume | 408290 ų |
| 包络体积 envelope_volume | 603980 ų |
| 水化壳体积 shell_volume | 89485 ų |
| 包络直径 envelope_diameter | 190.2 Å |
| 壳层 Rg shell_rg | 55.95 Å |
| 包络 Rg envelope_rg | 56.83 Å |
| 形状 Rg shape_rg | 58.59 Å |
| 总 Rg total_rg | 58.53 Å |
| 总原子数 total_atoms | 22881 |
| 残基数 n_residues | 3075 |
| 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 | 192.3 Å |
| Rg (实空间) rg_real | 58.62 Å |
| Rg 误差 (实空间) rg_real_error | 1.57 Å |
| I(0) (实空间) i0_real | 1.4830e+09 |
| I(0) 误差 (实空间) i0_real_error | 3.0750e+07 |
| Rg (倒空间) rg_reciprocal | 58.81 Å |
| I(0) (倒空间) i0_reciprocal | 1484000000.0000 |
| 解质量估计 total_estimate | 0.8409 |
| 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 | 78.3 Å |
| 偏度 Skewness skewness | 0.140 |
| 峰度 Kurtosis kurtosis | -0.507 |
| 角度范围 angular_range | — – 0.1350 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 62570000.0000 |
| 实空间数据点数 n_real_points | 28 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.748; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.686 |
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) 36 domains
SCOP 2.08 (12 domains)
| 结构域编号 domain_id | d1s4da_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.90 — Tetrapyrrole methylase |
| 超家族 Superfamily superfamily | c.90.1 — Tetrapyrrole methylase |
| 家族 Family family | c.90.1.1 — Tetrapyrrole methylase |
| 结构域编号 domain_id | d1s4db_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.90 — Tetrapyrrole methylase |
| 超家族 Superfamily superfamily | c.90.1 — Tetrapyrrole methylase |
| 家族 Family family | c.90.1.1 — Tetrapyrrole methylase |
| 结构域编号 domain_id | d1s4dd_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.90 — Tetrapyrrole methylase |
| 超家族 Superfamily superfamily | c.90.1 — Tetrapyrrole methylase |
| 家族 Family family | c.90.1.1 — Tetrapyrrole methylase |
| 结构域编号 domain_id | d1s4de_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.90 — Tetrapyrrole methylase |
| 超家族 Superfamily superfamily | c.90.1 — Tetrapyrrole methylase |
| 家族 Family family | c.90.1.1 — Tetrapyrrole methylase |
| 结构域编号 domain_id | d1s4df_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.90 — Tetrapyrrole methylase |
| 超家族 Superfamily superfamily | c.90.1 — Tetrapyrrole methylase |
| 家族 Family family | c.90.1.1 — Tetrapyrrole methylase |
| 结构域编号 domain_id | d1s4dg_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.90 — Tetrapyrrole methylase |
| 超家族 Superfamily superfamily | c.90.1 — Tetrapyrrole methylase |
| 家族 Family family | c.90.1.1 — Tetrapyrrole methylase |
| 结构域编号 domain_id | d1s4dh_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.90 — Tetrapyrrole methylase |
| 超家族 Superfamily superfamily | c.90.1 — Tetrapyrrole methylase |
| 家族 Family family | c.90.1.1 — Tetrapyrrole methylase |
| 结构域编号 domain_id | d1s4di_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.90 — Tetrapyrrole methylase |
| 超家族 Superfamily superfamily | c.90.1 — Tetrapyrrole methylase |
| 家族 Family family | c.90.1.1 — Tetrapyrrole methylase |
| 结构域编号 domain_id | d1s4dj_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.90 — Tetrapyrrole methylase |
| 超家族 Superfamily superfamily | c.90.1 — Tetrapyrrole methylase |
| 家族 Family family | c.90.1.1 — Tetrapyrrole methylase |
| 结构域编号 domain_id | d1s4dk_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.90 — Tetrapyrrole methylase |
| 超家族 Superfamily superfamily | c.90.1 — Tetrapyrrole methylase |
| 家族 Family family | c.90.1.1 — Tetrapyrrole methylase |
| 结构域编号 domain_id | d1s4dl_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.90 — Tetrapyrrole methylase |
| 超家族 Superfamily superfamily | c.90.1 — Tetrapyrrole methylase |
| 家族 Family family | c.90.1.1 — Tetrapyrrole methylase |
| 结构域编号 domain_id | d1s4dm_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.90 — Tetrapyrrole methylase |
| 超家族 Superfamily superfamily | c.90.1 — Tetrapyrrole methylase |
| 家族 Family family | c.90.1.1 — Tetrapyrrole methylase |
CATH v4.4 (24 domains)
| 结构域编号 domain_id | 1s4dA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1010 — Cobalt-precorrin-4 Transmethylase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, N-terminal domain |
| 结构域编号 domain_id | 1s4dA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, C-terminal domain |
| 结构域编号 domain_id | 1s4dB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1010 — Cobalt-precorrin-4 Transmethylase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, N-terminal domain |
| 结构域编号 domain_id | 1s4dB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, C-terminal domain |
| 结构域编号 domain_id | 1s4dD01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1010 — Cobalt-precorrin-4 Transmethylase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, N-terminal domain |
| 结构域编号 domain_id | 1s4dD02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, C-terminal domain |
| 结构域编号 domain_id | 1s4dE01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1010 — Cobalt-precorrin-4 Transmethylase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, N-terminal domain |
| 结构域编号 domain_id | 1s4dE02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, C-terminal domain |
| 结构域编号 domain_id | 1s4dF01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1010 — Cobalt-precorrin-4 Transmethylase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, N-terminal domain |
| 结构域编号 domain_id | 1s4dF02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, C-terminal domain |
| 结构域编号 domain_id | 1s4dG01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1010 — Cobalt-precorrin-4 Transmethylase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, N-terminal domain |
| 结构域编号 domain_id | 1s4dG02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, C-terminal domain |
| 结构域编号 domain_id | 1s4dH01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1010 — Cobalt-precorrin-4 Transmethylase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, N-terminal domain |
| 结构域编号 domain_id | 1s4dH02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, C-terminal domain |
| 结构域编号 domain_id | 1s4dI01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1010 — Cobalt-precorrin-4 Transmethylase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, N-terminal domain |
| 结构域编号 domain_id | 1s4dI02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, C-terminal domain |
| 结构域编号 domain_id | 1s4dJ01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1010 — Cobalt-precorrin-4 Transmethylase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, N-terminal domain |
| 结构域编号 domain_id | 1s4dJ02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, C-terminal domain |
| 结构域编号 domain_id | 1s4dK01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1010 — Cobalt-precorrin-4 Transmethylase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, N-terminal domain |
| 结构域编号 domain_id | 1s4dK02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, C-terminal domain |
| 结构域编号 domain_id | 1s4dL01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1010 — Cobalt-precorrin-4 Transmethylase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, N-terminal domain |
| 结构域编号 domain_id | 1s4dL02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, C-terminal domain |
| 结构域编号 domain_id | 1s4dM01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1010 — Cobalt-precorrin-4 Transmethylase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, N-terminal domain |
| 结构域编号 domain_id | 1s4dM02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tetrapyrrole methylase, C-terminal domain |