Download MendeleyCrystal structure of L-tyrosine decarboxylase MfnA (EC 4.1.1.25) (NP_247014.1) from METHANOCOCCUS JANNASCHII at 2.11 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3F9T | pdb_00003f9t
Crystal structure of L-tyrosine decarboxylase MfnA (EC 4.1.1.25) (NP_247014.1) from METHANOCOCCUS JANNASCHII at 2.11 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3F9T/pdb
- Classification: LYASE
- Organism(s): Methanocaldococcus jannaschii
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-11-14 Released: 2008-11-25
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.11 Å
- R-Value Free: 0.192 (Depositor), 0.190 (DCC)
- R-Value Work: 0.158 (Depositor), 0.160 (DCC)
- R-Value Observed: 0.160 (Depositor)
This is version 1.4 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 |
| L-tyrosine decarboxylase MfnA | 397 | Methanocaldococcus jannaschii | Mutation(s): 0 Gene Names: mfnA, MJ0050, NP_247014.1 EC: 4.1.1.25 (PDB Primary Data), 4.1.1.11 (UniProt) |  | |
UniProt | |||||
Find proteins for Q60358 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q60358 Go to UniProtKB: Q60358 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q60358 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PLP Query on PLP | C [auth A], F [auth B] | PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N |  | ||
| MPD Query on MPD | D [auth A], E [auth A], G [auth B] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-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: 2.11 Å
- R-Value Free: 0.192 (Depositor), 0.190 (DCC)
- R-Value Work: 0.158 (Depositor), 0.160 (DCC)
- R-Value Observed: 0.160 (Depositor)
Diffraction Data: https://doi.org/10.18430/M33F9T
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 85.276 | α = 90 |
| b = 104.128 | β = 90 |
| c = 119.915 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SOLVE | phasing |
| MolProbity | model building |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| MOSFLM | data reduction |
Entry History
Deposition Data
- Released Date: 2008-11-25 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2008-11-25
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
