3NIR Plant Protein date Jun 16, 2010
title Crystal Structure Of Small Protein Crambin At 0.48 A Resolut
authors A.Schmidt, M.Teeter, E.Weckert, V.S.Lamzin
compound source
Molecule: Crambin
Chain: A
Organism_scientific: Crambe Hispanica
Organism_common: Abyssinian Crambe, Abyssinian Kale
Organism_taxid: 3721
Strain: Subsp. Abyssinica
symmetry Space Group: P 1 21 1
R_factor 0.127 R_Free NULL
length a length b length c angle alpha angle beta angle gamma
22.329 18.471 40.769 90.00 90.55 90.00
method X-Ray Diffractionresolution 0.48 Å
ligand EOH enzyme

Primary referenceCrystal structure of small protein crambin at 0.48 A resolution., Schmidt A, Teeter M, Weckert E, Lamzin VS, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Apr 1;67(Pt, 4):424-8. Epub 2011 Mar 24. PMID:21505232
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (36 Kb) [Save to disk]
  • Biological Unit Coordinates (3nir.pdb1.gz) 32 Kb
  • LPC: Ligand-Protein Contacts for 3NIR
  • CSU: Contacts of Structural Units for 3NIR
  • Structure Factors (2501 Kb)
  • Retrieve 3NIR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NIR from S2C, [Save to disk]
  • Re-refined 3nir structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3NIR 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 3NIR
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3NIR, from MSDmotif at EBI
  • Fold representative 3nir from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nir] [3nir_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3NIR
  • Community annotation for 3NIR 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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