Download MendeleyCrystal structure of S-adenosylmethionine-dependent methyltransferase (NP_349143.1) from Clostridium acetobutylicum at 2.00 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
2P8J | pdb_00002p8j
Crystal structure of S-adenosylmethionine-dependent methyltransferase (NP_349143.1) from Clostridium acetobutylicum at 2.00 A resolution
- PDB DOI: https://doi.org/10.2210/pdb2P8J/pdb
- Classification: TRANSFERASE
- Organism(s): Clostridium acetobutylicum
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2007-03-22 Released: 2007-04-24
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.201 (Depositor), 0.210 (DCC)
- R-Value Work: 0.165 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.167 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 1.6 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 |
| S-adenosylmethionine-dependent methyltransferase | 209 | Clostridium acetobutylicum | Mutation(s): 4 Gene Names: NP_349143.1, CA_C2531 |  | |
UniProt | |||||
Find proteins for Q97G40 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)) Explore Q97G40 Go to UniProtKB: Q97G40 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q97G40 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PGE Query on PGE | I [auth B] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N |  | ||
| PEG Query on PEG | E [auth A], J [auth B], K [auth B] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| SO4 Query on SO4 | C [auth A], D [auth A], H [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | F [auth A] G [auth A] L [auth B] M [auth B] N [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.201 (Depositor), 0.210 (DCC)
- R-Value Work: 0.165 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.167 (Depositor)
Diffraction Data: https://doi.org/10.18430/M32P8J
Space Group: P 31 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 83.86 | α = 90 |
| b = 83.86 | β = 90 |
| c = 159.2 | γ = 120 |
| Software Name | Purpose |
|---|---|
| MolProbity | model building |
| SHELX | phasing |
| REFMAC | refinement |
| SCALEPACK | data scaling |
| PDB_EXTRACT | data extraction |
| MAR345 | data collection |
| HKL-2000 | data reduction |
| SHELXD | phasing |
| autoSHARP | phasing |
Entry History
Deposition Data
- Released Date: 2007-04-24 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2007-04-24
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.3: 2017-10-18
Changes: Refinement description - Version 1.4: 2017-10-25
Changes: Author supporting evidence - Version 1.5: 2023-01-25
Changes: Database references, Derived calculations - Version 1.6: 2024-10-30
Changes: Data collection, Refinement description, Structure summary
