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(-) Description

Title :  CRYSTAL STRUCTURE OF AN H-NOX PROTEIN FROM NOSTOC SP. PCC 7120, L66W MUTANT
 
Authors :  M. B. Winter, M. A. Herzik Jr. , J. Kuriyan, M. A. Marletta
Date :  15 Aug 11  (Deposition) - 09 Nov 11  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Heme-Based Sensor Domain, Gas Binding, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. B. Winter, M. A. Herzik, J. Kuriyan, M. A. Marletta
Tunnels Modulate Ligand Flux In A Heme Nitric Oxide/Oxygen Binding (H-Nox) Domain.
Proc. Natl. Acad. Sci. Usa V. 108 E881 2011
PubMed-ID: 21997213  |  Reference-DOI: 10.1073/PNAS.1114038108

(-) Compounds

Molecule 1 - ALR2278 PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ALR2278
    Mutation: YES
    Organism Scientific: NOSTOC SP.
    Organism Taxid: 103690
    Strain: PCC 7120 / UTEX 2576

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MLA1Ligand/IonMALONIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MLA-1Ligand/IonMALONIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MLA1Ligand/IonMALONIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:1 , TYR A:2 , TRP A:74 , THR A:78 , TYR A:83 , PHE A:97 , LEU A:101 , HIS A:105 , VAL A:108 , LEU A:115 , ARG A:116 , PRO A:118 , PHE A:120 , TYR A:134 , SER A:136 , ARG A:138 , LEU A:141 , MET A:144 , VAL A:145 , LEU A:148 , HOH A:214 , HOH A:245BINDING SITE FOR RESIDUE HEM A 500
2AC2SOFTWAREMET B:1 , TYR B:2 , VAL B:5 , TRP B:74 , THR B:78 , TYR B:83 , PHE B:97 , LEU B:101 , HIS B:105 , LEU B:115 , ARG B:116 , PRO B:118 , PHE B:120 , TYR B:134 , SER B:136 , ARG B:138 , VAL B:145 , LEU B:148 , HOH B:196 , HOH B:204BINDING SITE FOR RESIDUE HEM B 501
3AC3SOFTWAREHIS B:16 , HIS B:17 , LYS B:61 , ALA B:69 , HOH B:217 , HOH B:222 , HOH B:256 , HOH B:259BINDING SITE FOR RESIDUE MLA B 184

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TFD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TFD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TFD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TFD)

(-) Exons   (0, 0)

(no "Exon" information available for 3TFD)

(-) 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:183
 aligned with Q8YUQ7_NOSS1 | Q8YUQ7 from UniProtKB/TrEMBL  Length:189

    Alignment length:183
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   
         Q8YUQ7_NOSS1     1 MYGLVNKAIQDMISKHHGEDTWEAIKQKAGLEDIDFFVGMEAYSDDVTYHLVGAASEVLGKPAEELLIAFGEYWVTYTSEEGYGELLASAGDSLPEFMENLDNLHARVGLSFPQLRPPAFECQHTSSKSMELHYQSTRCGLAPMVLGLLHGLGKRFQTKVEVTQTAFRETGEDHDIFSIKYED 183
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhh......eeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhh..eeeeeeee........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tfd A   1 MYGLVNKAIQDMISKHHGEDTWEAIKQKAGLEDIDFFVGMEAYSDDVTYHLVGAASEVLGKPAEEWLIAFGEYWVTYTSEEGYGELLASAGDSLPEFMENLDNLHARVGLSFPQLRPPAFECQHTSSKSMELHYQSTRCGLAPMVLGLLHGLGKRFQTKVEVTQTAFRETGEDHDIFSIKYED 183
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   


Chain B from PDB  Type:PROTEIN  Length:182
 aligned with Q8YUQ7_NOSS1 | Q8YUQ7 from UniProtKB/TrEMBL  Length:189

    Alignment length:182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  
         Q8YUQ7_NOSS1     1 MYGLVNKAIQDMISKHHGEDTWEAIKQKAGLEDIDFFVGMEAYSDDVTYHLVGAASEVLGKPAEELLIAFGEYWVTYTSEEGYGELLASAGDSLPEFMENLDNLHARVGLSFPQLRPPAFECQHTSSKSMELHYQSTRCGLAPMVLGLLHGLGKRFQTKVEVTQTAFRETGEDHDIFSIKYE 182
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhh......eeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhh..eeeeeeee........eeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tfd B   1 MYGLVNKAIQDMISKHHGEDTWEAIKQKAGLEDIDFFVGMEAYSDDVTYHLVGAASEVLGKPAEEWLIAFGEYWVTYTSEEGYGELLASAGDSLPEFMENLDNLHARVGLSFPQLRPPAFECQHTSSKSMELHYQSTRCGLAPMVLGLLHGLGKRFQTKVEVTQTAFRETGEDHDIFSIKYE 182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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 3TFD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TFD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TFD)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8YUQ7_NOSS1 | Q8YUQ7)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  3tfd
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 Related Entries

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

UniProtKB/TrEMBL
        Q8YUQ7_NOSS1 | Q8YUQ7: 2o09 2o0c 2o0g 3l6j 3tf8 3tf9 3tfa 3tfe 3tff 3tfg 4iae 4iah 4iam 4jqh

(-) Related Entries Specified in the PDB File

2o09 2o0c 2o0g 3tf0 3tf1 3tf8 3tf9 3tfa 3tfe 3tff 3tfg