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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A DOMAIN FROM A POSSIBLE MEMBRANE PROTEIN OF BORDETELLA PARAPERTUSSIS
 
Authors :  K. Tan, C. Tesar, G. Cobb, A. Joachimiak, Midwest Center For Structu Genomics (Mcsg)
Date :  10 Aug 10  (Deposition) - 06 Oct 10  (Release) - 06 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Biol. Unit 2:  A,B  (2x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, C. Tesar, G. Cobb, A. Joachimiak
The Crystal Structure Of A Domain From A Possible Membrane Protein Of Bordetella Parapertussis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE MEMBRANE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: PPK1037
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 299-469
    Gene: BPP2278
    Organism Scientific: BORDETELLA PARAPERTUSSIS
    Organism Taxid: 519

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): AB
Biological Unit 2 (2x): AB
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 22)

Asymmetric Unit (4, 22)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG7Ligand/IonMAGNESIUM ION
3MSE6Mod. Amino AcidSELENOMETHIONINE
4SO47Ligand/IonSULFATE ION
Biological Unit 1 (3, 60)
No.NameCountTypeFull Name
1ADP8Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3MSE24Mod. Amino AcidSELENOMETHIONINE
4SO428Ligand/IonSULFATE ION
Biological Unit 2 (3, 30)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3MSE12Mod. Amino AcidSELENOMETHIONINE
4SO414Ligand/IonSULFATE ION
Biological Unit 3 (3, 15)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3MSE6Mod. Amino AcidSELENOMETHIONINE
4SO47Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:216 , HOH A:217 , HOH A:218 , HOH A:219 , HOH A:222 , GLU A:460BINDING SITE FOR RESIDUE MG A 1
02AC2SOFTWAREHOH A:201 , HOH A:210 , HOH A:215 , HOH A:221 , HOH A:227 , HIS A:365BINDING SITE FOR RESIDUE MG A 2
03AC3SOFTWAREHOH A:213 , ADP B:1 , HOH B:202 , HOH B:209 , HOH B:220BINDING SITE FOR RESIDUE MG A 5
04AC4SOFTWAREHOH A:285 , HOH A:286 , HOH A:287 , HOH A:288 , HOH A:289 , GLU A:449BINDING SITE FOR RESIDUE MG A 7
05AC5SOFTWAREHOH A:41 , HOH A:48 , HOH A:54 , HOH A:199 , HOH A:203 , HOH A:211 , HOH A:216 , HOH A:219 , HOH A:227 , HOH A:241 , THR A:339 , ASP A:343 , SER A:345 , HIS A:365 , SER A:366 , PHE A:367 , LEU A:441 , THR A:443 , ILE A:445 , ASP A:446 , ASP A:457 , HOH A:473 , MG B:6 , HOH B:207BINDING SITE FOR RESIDUE ADP A 470
06AC6SOFTWAREARG A:396 , ARG A:398 , ARG A:399 , ASN A:400 , SO4 A:471BINDING SITE FOR RESIDUE SO4 A 3
07AC7SOFTWAREARG A:372 , ARG B:372BINDING SITE FOR RESIDUE SO4 A 4
08AC8SOFTWARESO4 A:3 , HOH A:169 , HOH A:191 , HOH A:295 , HOH A:296 , ARG A:341BINDING SITE FOR RESIDUE SO4 A 471
09AC9SOFTWAREHOH B:224 , HOH B:231 , HOH B:233 , HOH B:239 , HOH B:279 , HIS B:365BINDING SITE FOR RESIDUE MG B 3
10BC1SOFTWAREHOH B:229 , HOH B:240 , HOH B:248 , HOH B:252 , HOH B:268 , GLU B:460BINDING SITE FOR RESIDUE MG B 4
11BC2SOFTWAREHOH A:199 , HOH A:211 , HOH A:291 , ADP A:470 , HOH B:207BINDING SITE FOR RESIDUE MG B 6
12BC3SOFTWAREMG A:5 , HOH A:213 , HOH B:91 , HOH B:96 , HOH B:196 , HOH B:200 , HOH B:202 , HOH B:205 , HOH B:209 , HOH B:224 , HOH B:225 , HOH B:240 , HOH B:248 , THR B:339 , ASP B:343 , SER B:345 , HIS B:365 , SER B:366 , PHE B:367 , LEU B:441 , THR B:443 , ILE B:445 , ASP B:446 , ASP B:457BINDING SITE FOR RESIDUE ADP B 1
13BC4SOFTWAREHOH B:278 , ARG B:341 , HOH B:479BINDING SITE FOR RESIDUE SO4 B 470
14BC5SOFTWAREARG B:396 , ARG B:398 , ARG B:399 , ASN B:400BINDING SITE FOR RESIDUE SO4 B 2
15BC6SOFTWAREHOH B:165 , HOH B:170 , SER B:333 , ARG B:335BINDING SITE FOR RESIDUE SO4 B 471
16BC7SOFTWAREHOH B:66 , HOH B:76 , HOH B:232 , SER B:345 , GLN B:359 , HOH B:480BINDING SITE FOR RESIDUE SO4 B 7

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OCM)

(-) 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:149
 aligned with Q7W867_BORPA | Q7W867 from UniProtKB/TrEMBL  Length:564

    Alignment length:149
                                   323       333       343       353       363       373       383       393       403       413       423       433       443       453         
         Q7W867_BORPA   314 AFGVEERNMVSGVLTLAERSIRSIMTPRTDVSWVNIDDDAATIRQQLTAAPHSFFPVCRGSLDEVVGIGRAKDLVADLITEGRVRRNRLRDPIIVHESIGILRLMDTLKRSRGQLVLVADEFGAIEGLVTPIDVFEAIAGEFPDEDELP 462
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh......ee.hhh..ee...hhhhhhhhhhhh...eeeee......eeeeeehhhhhhhhhhhh..hhhhh....eehhhhhhhhhhhhhhhh....eeee.....eeeeehhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ocm A 314 AFGVEERNmVSGVLTLAERSIRSImTPRTDVSWVNIDDDAATIRQQLTAAPHSFFPVCRGSLDEVVGIGRAKDLVADLITEGRVRRNRLRDPIIVHESIGILRLmDTLKRSRGQLVLVADEFGAIEGLVTPIDVFEAIAGEFPDEDELP 462
                                   323       333    |  343       353       363       373       383       393       403       413    |  423       433       443       453         
                                  322-MSE         338-MSE                                                                         418-MSE                                        


Chain B from PDB  Type:PROTEIN  Length:146
 aligned with Q7W867_BORPA | Q7W867 from UniProtKB/TrEMBL  Length:564

    Alignment length:146
                                   324       334       344       354       364       374       384       394       404       414       424       434       444       454      
         Q7W867_BORPA   315 FGVEERNMVSGVLTLAERSIRSIMTPRTDVSWVNIDDDAATIRQQLTAAPHSFFPVCRGSLDEVVGIGRAKDLVADLITEGRVRRNRLRDPIIVHESIGILRLMDTLKRSRGQLVLVADEFGAIEGLVTPIDVFEAIAGEFPDEDE 460
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------CBS-3ocmB01 B:388-453                                             ------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------CBS-3ocmB02 B:388-453                                             ------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhee.hhh..ee...hhhhhhhhhhhh...eeeee......eeeeeehhhhhhhhhhhh..hhhhh....eehhhhhhhhhhhhhhhhh...eeee.....eeeeehhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ocm B 315 FGVEERNmVSGVLTLAERSIRSImTPRTDVSWVNIDDDAATIRQQLTAAPHSFFPVCRGSLDEVVGIGRAKDLVADLITEGRVRRNRLRDPIIVHESIGILRLmDTLKRSRGQLVLVADEFGAIEGLVTPIDVFEAIAGEFPDEDE 460
                                   324       334   |   344       354       364       374       384       394       404       414   |   424       434       444       454      
                                 322-MSE         338-MSE                                                                         418-MSE
   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 3OCM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: CBS] (51)
(-)
Family: CBS (51)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q7W867_BORPA | Q7W867)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016614    oxidoreductase activity, acting on CH-OH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
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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