1d9d
CRYSTALL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH SHORT DNA FRAGMENT CARRYING 2'-0-AMINOPROPYL-RNA MODIFICATIONS 5'-D(TCG)-AP(AUC)-3'
1. Protein Identity and Related Structures Protein Identity & Related Structures
No usable UniProt protein identity is available for this entry.
七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白Chain接。
Assembly Composition of the Current Entry
| Assembly | Oligomeric State | 实体与Construct证据 | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein–DNA Monomer 蛋白 1 / DNA 1 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric | Entity 1：5'-D(*TP*CP*GP)-R(AP*(U31)P*(C31))-3' × 1 Entity 2：DNA POLYMERASE I × 1 缺少 UniProt 身份时不显示参考序列区间 | Non-standard monomer：Yes (specific site not provided by mmCIF) Entity 2Fragment：KLENOW FRAGMENT | ZN ZINC ION × 4 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 4 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.4；295 K；SODIUM CITRATE, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K | Resolution 2.18 Å R-free 0.238 |
The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.
SAXS scattering curve SAXS Profile
P(r) Distance Distribution P(r) Distribution
2. Structure Basics 2. Structure Basics
| Entry ID entry_id | 1d9d |
| Deposition date deposition_date | 1999-10-27 |
| Structure title title | CRYSTALL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH SHORT DNA FRAGMENT CARRYING 2'-0-AMINOPROPYL-RNA MODIFICATIONS 5'-D(TCG)-AP(AUC)-3' |
| Keywords keywords | ;KLENOW FRAGMENT, 2'-O-AMINOPROPYL NUCLEOTIDES, TRANSFERASE/DNA, RNA COMPLEX, TRANSFERASE-DNA ;; TRANSFERASE/DNA, RNA |
| Experimental Method method | X-RAY DIFFRACTION |
3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)
| Radius of gyration Rg (Guinier) rg_guinier | 27.85 Å |
| Radius of gyration Rg (electron density) rg_electron | 27.26 Å |
| Forward intensity I(0) i0 | 79947400.00 |
| Molecular weight molecular_weight | 69109.0 kDa |
| Excluded volume excluded_volume | 86095 ų |
| Envelope volume envelope_volume | 107540 ų |
| Hydration-shell volume shell_volume | 32934 ų |
| Envelope diameter envelope_diameter | 95.2 Å |
| Shell Rg shell_rg | 34.64 Å |
| Envelope Rg envelope_rg | 27.14 Å |
| Shape Rg shape_rg | 27.29 Å |
| Total Rg total_rg | 27.92 Å |
| Total atoms total_atoms | 4844 |
| Residues n_residues | 602 |
| Spherical-harmonic order n_harmonics | 20 |
| q range q_range | — – 0.5000 Å−1 |
| Data points n_points | 101 |
| Shell type shell_type | directional |
| Solvent electron density solvent_density | 0.3340 e/ų |
| Shell contrast contrast_shell | 0.0300 e/ų |
| CRYSOL version crysol_version | 4.1.3 |
4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)
| Maximum dimension Dmax dmax | 89.0 Å |
| Rg (real space) rg_real | 27.78 Å |
| Rg uncertainty (real space) rg_real_error | 0.57 Å |
| I(0) (real space) i0_real | 7.9950e+07 |
| I(0) uncertainty (real space) i0_real_error | 1.0760e+06 |
| Rg (reciprocal space) rg_reciprocal | 27.80 Å |
| I(0) (reciprocal space) i0_reciprocal | 79950000.0000 |
| Solution quality estimate total_estimate | 0.9001 |
| Solution quality rating solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) peaks n_peaks | 2 |
| Primary peak position r_peak_primary | 34.4 Å |
| Skewness Skewness skewness | 0.253 |
| Kurtosis Kurtosis kurtosis | -0.401 |
| Angular range angular_range | — – 0.2850 Å−1 |
| Current regularization parameter α current_alpha | 0.0000 |
| Highest regularization parameter α highest_alpha | 21350000.0000 |
| Real-space data points n_real_points | 58 |
| GNOM version gnom_version | 4.1.3 |
| Quality Criteria quality_criteria | AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.945 |
5. Crystallography and Experiment 5. Crystallography & Experiment
6. Entities and Polymers Entities & Polymers (6)
7. Fold Classification (SCOP + CATH) 6 domains
SCOP 2.08 (2 domains)
| Domain ID domain_id | d1d9da1 |
| Class class | c — Alpha and beta proteins (a/b) |
| Fold Fold fold | c.55 — Ribonuclease H-like motif |
| Superfamily Superfamily superfamily | c.55.3 — Ribonuclease H-like |
| Family Family family | c.55.3.5 — DnaQ-like 3'-5' exonuclease |
| Domain ID domain_id | d1d9da2 |
| Class class | e — Multi-domain proteins (alpha and beta) |
| Fold Fold fold | e.8 — DNA/RNA polymerases |
| Superfamily Superfamily superfamily | e.8.1 — DNA/RNA polymerases |
| Family Family family | e.8.1.1 — DNA polymerase I |
CATH v4.4 (4 domains)
| Domain ID domain_id | 1d9dA01 |
| Class class | 3 — Alpha Beta |
| Architecture architecture | 30 — 2-Layer Sandwich |
| Topology topology | 420 — Nucleotidyltransferase; domain 5 |
| Homologous superfamily homologous superfamily | 10 — Ribonuclease H-like superfamily/Ribonuclease H |
| Domain ID domain_id | 1d9dA02 |
| Class class | 1 — Mainly Alpha |
| Architecture architecture | 20 — Up-down Bundle |
| Topology topology | 1060 — Taq DNA Polymerase; Chain T, domain 4 |
| Homologous superfamily homologous superfamily | 10 — Taq DNA Polymerase; Chain T, domain 4 |
| Domain ID domain_id | 1d9dA03 |
| Class class | 3 — Alpha Beta |
| Architecture architecture | 30 — 2-Layer Sandwich |
| Topology topology | 70 — Alpha-Beta Plaits |
| Homologous superfamily homologous superfamily | 370 — |
| Domain ID domain_id | 1d9dA04 |
| Class class | 1 — Mainly Alpha |
| Architecture architecture | 10 — Orthogonal Bundle |
| Topology topology | 150 — DNA polymerase; domain 1 |
| Homologous superfamily homologous superfamily | 20 — 5' to 3' exonuclease, C-terminal subdomain |