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(-) Description

Title :  OXIDIZED FLAVODIIRON CORE OF ESCHERICHIA COLI FLAVORUBREDOXIN, INCLUDING THE FE-4SG ATOMS FROM ITS RUBREDOXIN DOMAIN
 
Authors :  C. V. Romao, P. T. Borges, J. B. Vicente, M. A. Carrondo, M. Teixeira, C. F
Date :  29 Jul 16  (Deposition) - 19 Oct 16  (Release) - 30 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  A  (2x)
Keywords :  Flavorubredoxin, Flavodiiron Protein, Diiron Center, Nitric Oxide Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. V. Romao, J. B. Vicente, P. T. Borges, B. L. Victor, P. Lamosa, E. Silva, L. Pereira, T. M. Bandeiras, C. M. Soares, M. A. Carrondo, D. Turner, M. Teixeira, C. Frazao
Structure Of Escherichia Coli Flavodiiron Nitric Oxide Reductase.
J. Mol. Biol. V. 428 4686 2016
PubMed-ID: 27725182  |  Reference-DOI: 10.1016/J.JMB.2016.10.008

(-) Compounds

Molecule 1 - ANAEROBIC NITRIC OXIDE REDUCTASE FLAVORUBREDOXIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NORV, FLRD, YGAI, YGAJ, YGAK, B2710, JW2680
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Other Details: FLAVORUBREDOXIN WAS MODELED FROM RESIDUE 2 TO 400, BECAUSE RESIDUES 401 TO 479 WERE NOT VISIBLE DUE TO DISORDER. HOWEVER, THE HEAVIER ATOMS FROM THE MISSING C-TERMINAL RUBREDOXIN DOMAIN, FE-4S, WERE DETECTED AND VALIDATED THROUGH ITS STEREOCHEMISTRY.
    Synonym: FLAVORB, FLAVODIIRON NITRIC OXIDE REDUCTASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 8)

Asymmetric Unit (7, 8)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2CAC1Ligand/IonCACODYLATE ION
3FE1Ligand/IonFE (III) ION
4FEO1Ligand/IonMU-OXO-DIIRON
5FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
6GOL1Ligand/IonGLYCEROL
7PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (6, 28)
No.NameCountTypeFull Name
1ACY4Ligand/IonACETIC ACID
2CAC4Ligand/IonCACODYLATE ION
3FE-1Ligand/IonFE (III) ION
4FEO4Ligand/IonMU-OXO-DIIRON
5FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
6GOL4Ligand/IonGLYCEROL
7PO48Ligand/IonPHOSPHATE ION
Biological Unit 2 (6, 14)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2CAC2Ligand/IonCACODYLATE ION
3FE-1Ligand/IonFE (III) ION
4FEO2Ligand/IonMU-OXO-DIIRON
5FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
6GOL2Ligand/IonGLYCEROL
7PO44Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:79 , GLU A:81 , ASP A:83 , HIS A:84 , HIS A:147 , ASP A:166 , HIS A:227 , PO4 A:503binding site for residue FEO A 501
2AC2SOFTWAREHIS A:23 , GLU A:81 , TRP A:148 , THR A:260 , MET A:261 , SER A:262 , ASN A:263 , ASN A:264 , THR A:265 , SER A:313 , THR A:314 , MET A:315 , ASN A:316 , ASN A:317 , SER A:345 , HIS A:346 , GLY A:347 , TRP A:348 , SER A:349 , GLY A:350 , TRP A:375 , HOH A:617 , HOH A:712 , HOH A:760 , HOH A:862binding site for residue FMN A 502
3AC3SOFTWAREHIS A:23 , GLU A:81 , ASP A:83 , HIS A:147 , ASP A:166 , HIS A:171 , TYR A:194 , ILE A:198 , HIS A:227 , FEO A:501binding site for residue PO4 A 503
4AC4SOFTWAREARG A:64 , HOH A:827binding site for residue PO4 A 504
5AC5SOFTWAREASP A:68 , ALA A:70 , ASP A:71 , ASP A:73 , HOH A:651binding site for residue CAC A 505
6AC6SOFTWAREHIS A:53 , GLY A:86binding site for residue ACY A 506
7AC7SOFTWARESER A:357 , MET A:367 , SER A:368 , HOH A:605 , HOH A:745binding site for residue GOL A 507
8AC8SOFTWARECYS A:428 , CYS A:431 , CYS A:461 , CYS A:464binding site for residue FE A 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LMC)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:146 -His A:147

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LMC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LMC)

(-) Exons   (0, 0)

(no "Exon" information available for 5LMC)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:403
                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eee..eee....ee....ee....eee..eeee...eeee...hhhhhhhhhhhhhhhhhhhhh.eee..........hhhhhhhhh....eeehhhhhhhhhhhhh.....eee.....eeeee..eeeeeee.........eeeee....eeeee............hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......eeee....ee...hhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhh.eeeee..ee..eehhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhh..ee...eeee...hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lmc A   2 SIVVKNNIHWVGQRDWEVRDFHGTEYKTLRGSSYNSYLIREEKNVLIDTVDHKFSREFVQNLRNEIDLADIDYIVINHAEEDHAGALTELMAQIPDTPIYCTANAIDSINGHHHHPEWNFNVVKTGDTLDIGNGKQLIFVETPMLHWPDSMMTYLTGDAVLFSNDAFGQHYCDEHLFNDEVDQTELFEQCQRYYANILTPFSRLVTPKITEILGFNLPVDMIATSHGVVWRDNPTQIVELYLKWAADYQEDRITIFYDTMSNNTRMMADAIAQGIAETDPRVAVKIFNVARSDKNEILTNVFRSKGVLVGTSTMNNVMMPKIAGLVEEMTGLRFRNKRASAFGSHGWSGGAVDRLSTRLQDAGFEMSLSLKAKWRPDQDALKLCREHGREIARQWALAPCCCC 464
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       428|||
                                                                                                                                                                                                                                                                                                                                                                                                                                        400||||
                                                                                                                                                                                                                                                                                                                                                                                                                                         428|||
                                                                                                                                                                                                                                                                                                                                                                                                                                          431||
                                                                                                                                                                                                                                                                                                                                                                                                                                           461|
                                                                                                                                                                                                                                                                                                                                                                                                                                            464
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5LMC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LMC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LMC)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NORV_ECOLI | Q46877: 2ms3 4d02 5lld

(-) Related Entries Specified in the PDB File

4d02 4D02 IS THE SAME PROTEIN BUT THE WITHOUT THE FE-4SG ATOM FROM RUBREDOXIN DOMAIN OF THE FLAVORUBREDOXIN.