1N13

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.191

Literature

Macromolecules
Sequence Display for 1N13

Classification: LYASE

Total Structure Weight: 108079.73

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
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
Gene Name(s): pdaD MJ0316

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

B, D, F, H, J, L AGMATINE
(4-AMINOBUTYL)GUANIDINE (Synonym)
C5 H14 N4
QYPPJABKJHAVHS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MRD
Query on MRD

B, D, F, H, J, L (4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
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: 1.4 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.191
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 56.46 α = 90.00
b = 92.88 β = 94.74
c = 87.11 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-10-16
  • Released Date: 2003-03-25
  • Deposition author(s): Tolbert, W.D., Graham, D.E., White, R.H., Ealick, S.E.

Revision History

  • Version 1_0: 2003-03-25

    Type: Initial release

  • Version 1_1: 2008-04-28

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance