Download MendeleyCrystal structure of the mutant H128N of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP
Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.To be published.
4LC8
Crystal structure of the mutant H128N of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP
- PDB DOI: https://doi.org/10.2210/pdb4LC8/pdb
- Classification: Lyase/Lyase Inhibitor
- Organism(s): Methanothermobacter thermautotrophicus str. Delta H
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2013-06-21 Released: 2013-07-03
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.32 Å
- R-Value Free: 0.178
- R-Value Work: 0.161
- R-Value Observed: 0.161
This is version 1.1 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 |
| Orotidine 5'-phosphate decarboxylase | 228 | Methanothermobacter thermautotrophicus str. Delta H | Mutation(s): 2 Gene Names: pyrF, MTH_129 EC: 4.1.1.23 |  | |
UniProt | |||||
Find proteins for O26232 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26232 Go to UniProtKB: O26232 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O26232 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| BMP Query on BMP | C [auth A], H [auth B] | 6-HYDROXYURIDINE-5'-PHOSPHATE C9 H13 N2 O10 P UDOBICLZEKUKCV-YXZULKJRSA-N |  | ||
| EDO Query on EDO | K [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| CL Query on CL | D [auth A], E [auth A], F [auth A], I [auth B], J [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| MG Query on MG | G [auth A], L [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.32 Å
- R-Value Free: 0.178
- R-Value Work: 0.161
- R-Value Observed: 0.161
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 59.958 | α = 90 |
| b = 63.703 | β = 115.3 |
| c = 61.74 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CBASS | data collection |
| BALBES | phasing |
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2013-07-03 Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.
Revision History (Full details and data files)
- Version 1.0: 2013-07-03
Type: Initial release - Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
