1MT1

The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannaschii

Structural Biology Knowledgebase: 1MT1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.190

Literature

Macromolecules
Sequence Display for 1MT1

Classification: LYASE

Total Structure Weight: 108693.44

Macromolecule Entities
Molecule Chains Length Organism Details
PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE BETA CHAIN A, C, E..., G, I, KA, C, E, G, I, K 52 Methanocaldococcus jannaschii EC#: 4.1.1.19 IUBMB
Mutation: M1M
Gene Name(s): pdaD MJ0316
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE ALPHA CHAIN B, D, F..., H, J, LB, D, F, H, J, L 113 Methanocaldococcus jannaschii EC#: 4.1.1.19 IUBMB
Mutation: S53X, M55M, M69M, M108M, M126M, M133M
Gene Name(s): pdaD MJ0316

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AG2
Query on AG2

A, B, C, G, K AGMATINE
(4-AMINOBUTYL)GUANIDINE (Synonym)
C5 H14 N4
QYPPJABKJHAVHS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C, D, E, F, G, H, I, J, K, L L-PEPTIDE LINKING C5 H11 N O2 Se MET
PYR
Query on PYR
B, D, F, H, J, L NON-POLYMER C3 H4 O3 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.190
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 56.77 α = 90.00
b = 92.99 β = 94.84
c = 87.23 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-09-20
  • Released Date: 2003-03-25
  • Deposition author(s): Tolbert, W.D., Graham, D.E., White, R.H., Ealick, S.E.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4