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(-) Description

Title :  CRYSTAL STRUCTURE OF AN H-NOX PROTEIN FROM T. TENGCONGENSIS UNDER 6 ATM OF XENON
 
Authors :  M. B. Winter, M. A. Herzik Jr. , J. Kuriyan, M. A. Marletta
Date :  15 Aug 11  (Deposition) - 09 Nov 11  (Release) - 09 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Heme-Based Methyl-Accepting Chemotaxis Protein, 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 - METHYL-ACCEPTING CHEMOTAXIS PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: N-TERMINAL DOMAIN (UNP RESIDUES 1-188)
    Gene: TAR4, TTE0680
    Organism Scientific: CALDANAEROBACTER SUBTERRANEUS SUBSP. TENGCONGENSIS
    Organism Taxid: 119072

 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  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3OXY2Ligand/IonOXYGEN MOLECULE
4XE4Ligand/IonXENON
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3OXY1Ligand/IonOXYGEN MOLECULE
4XE-1Ligand/IonXENON
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3OXY1Ligand/IonOXYGEN MOLECULE
4XE-1Ligand/IonXENON

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:1 , LYS A:2 , ILE A:5 , PHE A:78 , TYR A:85 , MET A:98 , HIS A:102 , LEU A:105 , THR A:113 , PRO A:114 , MET A:129 , TYR A:131 , SER A:133 , ARG A:135 , MET A:137 , TYR A:140 , LEU A:144 , HOH A:192 , HOH A:214 , OXY A:501BINDING SITE FOR RESIDUE HEM A 500
2AC2SOFTWAREILE A:5 , PHE A:78 , TYR A:140 , HEM A:500BINDING SITE FOR RESIDUE OXY A 501
3AC3SOFTWARELYS A:2 , THR A:4 , PHE A:82 , LEU A:105 , HOH A:269 , SER B:84 , HOH B:199BINDING SITE FOR RESIDUE ACT A 191
4AC4SOFTWAREMET B:1 , LYS B:2 , ILE B:5 , PHE B:78 , TYR B:85 , MET B:98 , HIS B:102 , LEU B:105 , THR B:113 , PRO B:114 , LEU B:117 , TYR B:131 , SER B:133 , ARG B:135 , MET B:137 , TYR B:140 , LEU B:144 , HOH B:191 , HOH B:245 , OXY B:504BINDING SITE FOR RESIDUE HEM B 503
5AC5SOFTWAREPHE B:78 , TYR B:140 , LEU B:144 , HEM B:503BINDING SITE FOR RESIDUE OXY B 504
6AC6SOFTWAREILE B:10BINDING SITE FOR RESIDUE XE B 190

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TF1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TF1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TF1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TF1)

(-) Exons   (0, 0)

(no "Exon" information available for 3TF1)

(-) 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:188
 aligned with Q8RBX6_CALS4 | Q8RBX6 from UniProtKB/TrEMBL  Length:602

    Alignment length:188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
         Q8RBX6_CALS4     1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVHLQLTKMIKGATPPRLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
               SCOP domains d3tf1a_ A: Methyl-accepting chemotaxis protein                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..........eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tf1 A   1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVHLQLTKMIKGATPPRLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
                                    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:188
 aligned with Q8RBX6_CALS4 | Q8RBX6 from UniProtKB/TrEMBL  Length:602

    Alignment length:188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
         Q8RBX6_CALS4     1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVHLQLTKMIKGATPPRLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
               SCOP domains d3tf1b_ B: Methyl-accepting chemotaxis protein                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh........eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tf1 B   1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVHLQLTKMIKGATPPRLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   Legend:   → Mismatch (orange background)
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  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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TF1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TF1)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8RBX6_CALS4 | Q8RBX6)
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.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/TrEMBL
        Q8RBX6_CALS4 | Q8RBX6: 1u4h 1u55 1u56 1xbn 3eee 3iqb 3lah 3lai 3m0b 3nvr 3nvu 3sj5 3tf0 4fdk 4it2 5jru 5jrv 5jrx

(-) Related Entries Specified in the PDB File

1u4h 1u55 1u56 3tf0 3tf8 3tf9 3tfa 3tfd 3tfe 3tff 3tfg