Download MendeleyCrystal structure of methylated RPA0582 protein
Sledz, P., Niedzialkowska, E., Chruszcz, M., Porebski, P., Yim, V., Kudritska, M., Zimmerman, M.D., Evdokimova, E., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W.To be published.
3HHL
Crystal structure of methylated RPA0582 protein
- PDB DOI: 10.2210/pdb3HHL/pdb
- Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
- Organism(s): Rhodopseudomonas palustris
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-05-15 Released: 2009-07-07
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.65 Å
- R-Value Free: 0.206
- R-Value Work: 0.178
- R-Value Observed: 0.180
wwPDB Validation 3D Report Full Report
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| RPA0582 | A | 143 | Rhodopseudomonas palustris | Mutation(s): 0 Gene Names: RPA0582 |  |
UniProt | |||||
Find proteins for Q6NC90 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NC90 Go to UniProtKB: Q6NC90 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q6NC90 | ||||
Protein Feature ViewExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| RPA0582 | B | 143 | Rhodopseudomonas palustris | Mutation(s): 0 Gene Names: RPA0582 |  |
UniProt | |||||
Find proteins for Q6NC90 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NC90 Go to UniProtKB: Q6NC90 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q6NC90 | ||||
Protein Feature ViewExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| RPA0582 | C | 143 | Rhodopseudomonas palustris | Mutation(s): 0 Gene Names: RPA0582 |  |
UniProt | |||||
Find proteins for Q6NC90 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NC90 Go to UniProtKB: Q6NC90 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q6NC90 | ||||
Protein Feature ViewExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| RPA0582 | D | 143 | Rhodopseudomonas palustris | Mutation(s): 0 Gene Names: RPA0582 |  |
UniProt | |||||
Find proteins for Q6NC90 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NC90 Go to UniProtKB: Q6NC90 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q6NC90 | ||||
Protein Feature ViewExpand | |||||
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Small Molecules
| Ligands 9 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 2PE Query on 2PE | EA [auth D], J [auth A] | NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N |  | Ligand Interaction | |
| PE8 Query on PE8 | R [auth B], Z [auth C] | 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C16 H34 O9 GLZWNFNQMJAZGY-UHFFFAOYSA-N |  | Ligand Interaction | |
| 1PE Query on 1PE | T [auth B] | PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N |  | Ligand Interaction | |
| PG4 Query on PG4 | CA [auth D], W [auth C] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N |  | Ligand Interaction | |
| PGE Query on PGE | I [auth A], Q [auth B], Y [auth C] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N |  | Ligand Interaction | |
| PEG Query on PEG | DA [auth D], H [auth A], K [auth A], N [auth B], O [auth B], | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | Ligand Interaction | |
| SO4 Query on SO4 | E [auth A], F [auth A], U [auth C] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | Ligand Interaction | |
| GOL Query on GOL | AA [auth C], FA [auth D], L [auth A], S [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | Ligand Interaction | |
| CL Query on CL | BA [auth D], G [auth A], M [auth B], V [auth C] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | Ligand Interaction | |
| Modified Residues 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MLY Query on MLY | A | L-PEPTIDE LINKING | C8 H18 N2 O2 |  | LYS |
| MLZ Query on MLZ | A | L-PEPTIDE LINKING | C7 H16 N2 O2 |  | LYS |
| MSE Query on MSE | A | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.65 Å
- R-Value Free: 0.206
- R-Value Work: 0.178
- R-Value Observed: 0.180
- Space Group: H 3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 193.012 | α = 90 |
| b = 193.012 | β = 90 |
| c = 117.965 | γ = 120 |
| Software Name | Purpose |
|---|---|
| HKL-3000 | data collection |
| MOLREP | phasing |
| REFMAC | refinement |
| Coot | model building |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2009-07-07 Deposition Author(s): Sledz, P., Niedzialkowska, E., Chruszcz, M., Porebski, P., Yim, V., Kudritska, M., Zimmerman, M.D., Evdokimova, E., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-07-07
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
