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 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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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) 

Literature

Crystal 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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 92.04 kDa 
• Atom Count: 6,771 
• Modeled Residue Count: 786 
• Deposited Residue Count: 794 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-tyrosine decarboxylase MfnA	A, B	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], F [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
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	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 Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-25 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• 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