1OGY	Oxidoreductase	date	May 19, 2003
title	Crystal Structure Of The Heterodimeric Nitrate Reductase Fro Rhodobacter Sphaeroides
authors	P.Arnoux, M.Sabaty, J.Alric, B.Frangioni, B.Guigliarelli, J.M.Ad D.Pignol
compound		source
Molecule: Periplasmic Nitrate Reductase Chain: A, C, E, G, I, K, M, O Fragment: Catalytic Subunit, Residues 30-831 Synonym: Nitrate Reductase Ec: 1.7.99.4 Engineered: Yes		Organism_scientific: Rhodobacter Sphaeroides Organism_taxid: 1063 Expression_system: Rhodobacter Sphaeroides Expression_system_taxid: 1063
Molecule: Diheme Cytochrome C Napb Molecule: Nitrate Reduct Chain: B, D, F, H, J, L, N, P Fragment: Cytochrome Subunit, Residues 25-154 Engineered: Yes		Organism_scientific: Rhodobacter Sphaeroides Organism_taxid: 1063 Expression_system: Rhodobacter Sphaeroides Expression_system_taxid: 1063
symmetry	Space Group: P 1 21 1	R_factor 0.250 R_Free 0.269
crystal cell	length a length b length c angle alpha angle beta angle gamma 123.000 225.200 154.600 90.00 92.10 90.00
method	X-Ray Diffraction	resolution	3.20 Å
ligand	HEC, MGD, MO, SF4	enzyme	Oxidoreductase E.C.1.7.99.4 BRENDA
Gene Ontology	Chain Function Process Component F, N, L, J, P, B, H, D K, E, M, C, A, O, I, G electron transfer activity
Primary reference	Structural and redox plasticity in the heterodimeric periplasmic nitrate reductase., Arnoux P, Sabaty M, Alric J, Frangioni B, Guigliarelli B, Adriano JM, Pignol D, Nat Struct Biol 2003 Nov;10(11):928-34. Epub 2003 Oct 5. PMID:14528294

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1191 Kb) [Save to disk] Biological Unit Coordinates (1ogy.pdb1.gz) 160 Kb Biological Unit Coordinates (1ogy.pdb2.gz) 160 Kb Biological Unit Coordinates (1ogy.pdb3.gz) 161 Kb Biological Unit Coordinates (1ogy.pdb4.gz) 161 Kb Biological Unit Coordinates (1ogy.pdb5.gz) 161 Kb Biological Unit Coordinates (1ogy.pdb6.gz) 161 Kb Biological Unit Coordinates (1ogy.pdb7.gz) 162 Kb Biological Unit Coordinates (1ogy.pdb8.gz) 161 Kb LPC: Ligand-Protein Contacts for 1OGY CSU: Contacts of Structural Units for 1OGY Likely Quarternary Molecular Structure file(s) for 1OGY Structure Factors (1113 Kb) Retrieve 1OGY in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1OGY from S2C, [Save to disk] Re-refined 1ogy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1OGY 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 1OGY

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 3D motif for 1OGY, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1ogya2, region A:12-681 [Jmol] [rasmolscript] [script source]     - Domain d1ogya1, region A:682-801 [Jmol] [rasmolscript] [script source]     - Domain d1ogyb_, region B [Jmol] [rasmolscript] [script source]     - Domain d1ogyc2, region C:12-681 [Jmol] [rasmolscript] [script source]     - Domain d1ogyc1, region C:682-801 [Jmol] [rasmolscript] [script source]     - Domain d1ogyd_, region D [Jmol] [rasmolscript] [script source]     - Domain d1ogye2, region E:12-681 [Jmol] [rasmolscript] [script source]     - Domain d1ogye1, region E:682-801 [Jmol] [rasmolscript] [script source]     - Domain d1ogyf_, region F [Jmol] [rasmolscript] [script source]     - Domain d1ogyg2, region G:12-681 [Jmol] [rasmolscript] [script source]     - Domain d1ogyg1, region G:682-801 [Jmol] [rasmolscript] [script source]     - Domain d1ogyh_, region H [Jmol] [rasmolscript] [script source]     - Domain d1ogyi2, region I:12-681 [Jmol] [rasmolscript] [script source]     - Domain d1ogyi1, region I:682-801 [Jmol] [rasmolscript] [script source]     - Domain d1ogyj_, region J [Jmol] [rasmolscript] [script source]     - Domain d1ogyk2, region K:12-681 [Jmol] [rasmolscript] [script source]     - Domain d1ogyk1, region K:682-801 [Jmol] [rasmolscript] [script source]     - Domain d1ogyl_, region L [Jmol] [rasmolscript] [script source]     - Domain d1ogym2, region M:12-681 [Jmol] [rasmolscript] [script source]     - Domain d1ogym1, region M:682-801 [Jmol] [rasmolscript] [script source]     - Domain d1ogyn_, region N [Jmol] [rasmolscript] [script source]     - Domain d1ogyo2, region O:12-681 [Jmol] [rasmolscript] [script source]     - Domain d1ogyo1, region O:682-801 [Jmol] [rasmolscript] [script source]     - Domain d1ogyp_, region P [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ogy_K] [1ogy_D] [1ogy_L] [1ogy_C] [1ogy_M] [1ogy_O] [1ogy_P] [1ogy] [1ogy_A] [1ogy_N] [1ogy_H] [1ogy_J] [1ogy_I] [1ogy_E] [1ogy_F] [1ogy_B] [1ogy_G] SWISS-PROT database: [Q53176] [Q53177] Domain organization of [NAPA_RHOS4] [NAPB_RHOS4] by SWISSPFAM Domain found in 1OGY: [Molybdop_Fe4S4 ] by SMART

Other resources with information on 1OGY

Community annotation for 1OGY at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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