1N13 Lyase date Oct 16, 2002
title The Crystal Structure Of Pyruvoyl-Dependent Arginine Decarbo From Methanococcus Jannashii
authors W.D.Tolbert, D.E.Graham, R.H.White, S.E.Ealick
compound source
Molecule: Pyruvoyl-Dependent Arginine Decarboxylase Beta Ch
Chain: A, C, E, G, I, K
Synonym: Pvlargdc
Ec: 4.1.1.19
Engineered: Yes
Organism_scientific: Methanocaldococcus Jannaschii
Organism_taxid: 2190
Gene: Mj0316
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codon-Plus(De3)-Ril (Stratag
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet19b (Novagen)

Molecule: Pyruvoyl-Dependent Arginine Decarboxylase Alpha C
Chain: B, D, F, H, J, L
Synonym: Pvlargdc
Ec: 4.1.1.19
Engineered: Yes

Organism_scientific: Methanocaldococcus Jannaschii
Organism_taxid: 2190
Gene: Mj0316
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codon-Plus(De3)-Ril (Stratag
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet19b (Novagen)
symmetry Space Group: P 1 21 1
R_factor 0.192 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.460 92.880 87.110 90.00 94.74 90.00
method X-Ray Diffractionresolution 1.40 Å
ligand AG2, MRD, PYR enzyme Lyase E.C.4.1.1.19 BRENDA
related structures by homologous chain: 1N2M
Gene
Ontology
ChainFunctionProcessComponent
A, K, E, C, I, G


F, J, B, H, D, L


Primary referencePyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii: crystal structures of the self-cleaved and S53A proenzyme forms., Tolbert WD, Graham DE, White RH, Ealick SE, Structure (Camb) 2003 Mar;11(3):285-94. PMID:12623016
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (168 Kb) [Save to disk]
  • Biological Unit Coordinates (1n13.pdb1.gz) 84 Kb
  • Biological Unit Coordinates (1n13.pdb2.gz) 82 Kb
  • LPC: Ligand-Protein Contacts for 1N13
  • CSU: Contacts of Structural Units for 1N13
  • Likely Quarternary Molecular Structure file(s) for 1N13
  • Structure Factors (1189 Kb)
  • Retrieve 1N13 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1N13 from S2C, [Save to disk]
  • Re-refined 1n13 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1N13 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1N13
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1N13 1N13A 1N13B 1N13C 1N13D 1N13E 1N13F 1N13G 1N13H 1N13I 1N13J 1N13K 1N13L from the CEP Server.
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1N13, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1n13.1, region A:,B [Jmol] [rasmolscript] [script source]
        - Domain d1n13.2, region C:,D [Jmol] [rasmolscript] [script source]
        - Domain d1n13.3, region E:,F [Jmol] [rasmolscript] [script source]
        - Domain d1n13.4, region G:,H [Jmol] [rasmolscript] [script source]
        - Domain d1n13.5, region I:,J [Jmol] [rasmolscript] [script source]
        - Domain d1n13.6, region K:,L [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1n13_F] [1n13_A] [1n13_E] [1n13] [1n13_J] [1n13_G] [1n13_L] [1n13_C] [1n13_D] [1n13_I] [1n13_B] [1n13_H] [1n13_K]
  • SWISS-PROT database: [Q57764]
  • Domain organization of [PDAD_METJA] by SWISSPFAM
  • Other resources with information on 1N13
  • Community annotation for 1N13 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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