Download MendeleyCrystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate
Fedorov, A.A., Fedorov, E.V., Chan, K.K., Gerlt, J.A., Almo, S.C.To be published.
4NX5
Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate
- PDB DOI: https://doi.org/10.2210/pdb4NX5/pdb
- Classification: LYASE
- Organism(s): Methanothermobacter thermautotrophicus
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2013-12-08 Released: 2013-12-25
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.59 Å
- R-Value Free: 0.168
- R-Value Work: 0.148
- R-Value Observed: 0.148
Starting Model: experimental
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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 | Mutation(s): 1 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 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| UP6 Query on UP6 | C [auth A], G [auth B] | 6-AZA URIDINE 5'-MONOPHOSPHATE C8 H12 N3 O9 P LRVZOSYMNMNQFR-SHUUEZRQSA-N |  | ||
| GOL Query on GOL | J [auth B], K [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | F [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| CL Query on CL | D [auth A], E [auth A], H [auth B], I [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| MG Query on MG | L [auth B], M [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.59 Å
- R-Value Free: 0.168
- R-Value Work: 0.148
- R-Value Observed: 0.148
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 59.737 | α = 90 |
| b = 64.148 | β = 115.36 |
| c = 61.527 | γ = 90 |
| Software Name | Purpose |
|---|---|
| ADSC | data collection |
| BALBES | phasing |
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2013-12-25 Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Chan, K.K., Gerlt, J.A., Almo, S.C.
Revision History (Full details and data files)
- Version 1.0: 2013-12-25
Type: Initial release - Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
