Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE AND METAL-LOADING OF A SOLUBLE PERIPLASM CUPRO-PROTEIN: APO-CUCA-CLOSED (SEMET)
 
Authors :  K. J. Waldron, S. J. Firbank, S. J. Dainty, M. Perez-Rama, S. Tottey, N. J
Date :  20 Jul 10  (Deposition) - 11 Aug 10  (Release) - 18 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Metal Binding Protein, Cupin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Waldron, S. J. Firbank, S. J. Dainty, M. Perez-Rama, S. Tottey, N. J. Robinson
Structure And Metal Loading Of A Soluble Periplasm Cuproprotein.
J. Biol. Chem. V. 285 32504 2010
PubMed-ID: 20702411  |  Reference-DOI: 10.1074/JBC.M110.153080

(-) Compounds

Molecule 1 - SLL1785 PROTEIN
    Atcc: 27184
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Fragment: RESIDUES 31-268
    Organism Scientific: SYNECHOCYSTIS SP. PCC 6803
    Organism Taxid: 1148
    Synonym: CUCA

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 32)

Asymmetric Unit (1, 32)
No.NameCountTypeFull Name
1MSE32Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2XLF)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:65 -A:267
2B:65 -B:267
3C:65 -C:267
4D:65 -D:267

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XLF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XLF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XLF)

(-) Exons   (0, 0)

(no "Exon" information available for 2XLF)

(-) 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:233
 aligned with P73600_SYNY3 | P73600 from UniProtKB/TrEMBL  Length:268

    Alignment length:233
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265   
         P73600_SYNY3    36 HTFDDIPMPKLADPLLIYTPANEIFDIASCSAKDIGFAIAHAQIPPGGGPMPHIHYFINEWFWTPEGGIELFHSTKQYPNMDELPVVGGAGRGDLYSIQSEPKQLIYSPNHYMHGFVNPTDKTLPIVFVWMRNEVAPDFPYHDGGMREYFQAVGPRITDLNNLPELTNAQRAAFASEAPKYGINQSSYFMEYVNTISDKLPAQIAKLKNDKDLERMVEVIEAFNRGDKSVTCS 268
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeee...eeeeeeeeee..eeeeeeeeee........eee..eeeeee......eeeeeeee...............eeeeeee.....eeee...eeeeee......eeeeeeeee............hhhhhhhhhh............hhhhhhhhhhhhhhh.eee.......eeeee...hhhhhh..hhhhhhhhhhhhhhhhhh....ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xlf A  36 HTFDDIPmPKLADPLLIYTPANEIFDIASCSAKDIGFAIAHAQIPPGGGPmPHIHYFINEWFWTPEGGIELFHSTKQYPNmDELPVVGGAGRGDLYSIQSEPKQLIYSPNHYmHGFVNPTDKTLPIVFVWmRNEVAPDFPYHDGGmREYFQAVGPRITDLNNLPELTNAQRAAFASEAPKYGINQSSYFmEYVNTISDKLPAQIAKLKNDKDLERmVEVIEAFNRGDKSVTCS 268
                                   |45        55        65        75        85|       95       105       115|      125       135       145  |    155       165|      175     | 185       195       205       215       225       235       245     | 255       265   
                                  43-MSE                                     86-MSE                       116-MSE                         148-MSE           166-MSE        181-MSE                                     225-MSE                   251-MSE             


Chain B from PDB  Type:PROTEIN  Length:233
 aligned with P73600_SYNY3 | P73600 from UniProtKB/TrEMBL  Length:268

    Alignment length:233
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265   
         P73600_SYNY3    36 HTFDDIPMPKLADPLLIYTPANEIFDIASCSAKDIGFAIAHAQIPPGGGPMPHIHYFINEWFWTPEGGIELFHSTKQYPNMDELPVVGGAGRGDLYSIQSEPKQLIYSPNHYMHGFVNPTDKTLPIVFVWMRNEVAPDFPYHDGGMREYFQAVGPRITDLNNLPELTNAQRAAFASEAPKYGINQSSYFMEYVNTISDKLPAQIAKLKNDKDLERMVEVIEAFNRGDKSVTCS 268
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeee...eeeeeeeeee..eeeeeeeeee........eee..eeeeee......eeeeeeee...............eeeeeee.....eeee...eeeeee......eeeeeeeee............hhhhhhhhhh............hhhhhhhhhhhhhhh.eee..hhhh.eeeee...hhhhhh..hhhhhhhhhhhhhhhhhh....ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xlf B  36 HTFDDIPmPKLADPLLIYTPANEIFDIASCSAKDIGFAIAHAQIPPGGGPmPHIHYFINEWFWTPEGGIELFHSTKQYPNmDELPVVGGAGRGDLYSIQSEPKQLIYSPNHYmHGFVNPTDKTLPIVFVWmRNEVAPDFPYHDGGmREYFQAVGPRITDLNNLPELTNAQRAAFASEAPKYGINQSSYFmEYVNTISDKLPAQIAKLKNDKDLERmVEVIEAFNRGDKSVTCS 268
                                   |45        55        65        75        85|       95       105       115|      125       135       145  |    155       165|      175     | 185       195       205       215       225       235       245     | 255       265   
                                  43-MSE                                     86-MSE                       116-MSE                         148-MSE           166-MSE        181-MSE                                     225-MSE                   251-MSE             


Chain C from PDB  Type:PROTEIN  Length:233
 aligned with P73600_SYNY3 | P73600 from UniProtKB/TrEMBL  Length:268

    Alignment length:233
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265   
         P73600_SYNY3    36 HTFDDIPMPKLADPLLIYTPANEIFDIASCSAKDIGFAIAHAQIPPGGGPMPHIHYFINEWFWTPEGGIELFHSTKQYPNMDELPVVGGAGRGDLYSIQSEPKQLIYSPNHYMHGFVNPTDKTLPIVFVWMRNEVAPDFPYHDGGMREYFQAVGPRITDLNNLPELTNAQRAAFASEAPKYGINQSSYFMEYVNTISDKLPAQIAKLKNDKDLERMVEVIEAFNRGDKSVTCS 268
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee.....eeeeeeeee..eeeeeeeeee........eee..eeeeee......eeeeeeee...............eeeeeee.....eeee...eeeeee......eeeeeeeee............hhhhhhhhhh............hhhhhhhhhhhhhhh.eee..hhhh.eeeee...hhhhhh..hhhhhhhhhhhhhhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xlf C  36 HTFDDIPmPKLADPLLIYTPANEIFDIASCSAKDIGFAIAHAQIPPGGGPmPHIHYFINEWFWTPEGGIELFHSTKQYPNmDELPVVGGAGRGDLYSIQSEPKQLIYSPNHYmHGFVNPTDKTLPIVFVWmRNEVAPDFPYHDGGmREYFQAVGPRITDLNNLPELTNAQRAAFASEAPKYGINQSSYFmEYVNTISDKLPAQIAKLKNDKDLERmVEVIEAFNRGDKSVTCS 268
                                   |45        55        65        75        85|       95       105       115|      125       135       145  |    155       165|      175     | 185       195       205       215       225       235       245     | 255       265   
                                  43-MSE                                     86-MSE                       116-MSE                         148-MSE           166-MSE        181-MSE                                     225-MSE                   251-MSE             


Chain D from PDB  Type:PROTEIN  Length:233
 aligned with P73600_SYNY3 | P73600 from UniProtKB/TrEMBL  Length:268

    Alignment length:233
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265   
         P73600_SYNY3    36 HTFDDIPMPKLADPLLIYTPANEIFDIASCSAKDIGFAIAHAQIPPGGGPMPHIHYFINEWFWTPEGGIELFHSTKQYPNMDELPVVGGAGRGDLYSIQSEPKQLIYSPNHYMHGFVNPTDKTLPIVFVWMRNEVAPDFPYHDGGMREYFQAVGPRITDLNNLPELTNAQRAAFASEAPKYGINQSSYFMEYVNTISDKLPAQIAKLKNDKDLERMVEVIEAFNRGDKSVTCS 268
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeee...eeeeeeeeee..eeeeeeeeee........eee..eeeeeee.....eeeeeeee...............eeeeeee....eeeee...eeeeee......eeeeeeeee............hhhhhhhhhh............hhhhhhhhhhhhhhh.eee.......eeeee...hhhhhhh.hhhhhhhhhhhhhhhhhh....ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xlf D  36 HTFDDIPmPKLADPLLIYTPANEIFDIASCSAKDIGFAIAHAQIPPGGGPmPHIHYFINEWFWTPEGGIELFHSTKQYPNmDELPVVGGAGRGDLYSIQSEPKQLIYSPNHYmHGFVNPTDKTLPIVFVWmRNEVAPDFPYHDGGmREYFQAVGPRITDLNNLPELTNAQRAAFASEAPKYGINQSSYFmEYVNTISDKLPAQIAKLKNDKDLERmVEVIEAFNRGDKSVTCS 268
                                   |45        55        65        75        85|       95       105       115|      125       135       145  |    155       165|      175     | 185       195       205       215       225       235       245     | 255       265   
                                  43-MSE                                     86-MSE                       116-MSE                         148-MSE           166-MSE        181-MSE                                     225-MSE                   251-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 2XLF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XLF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2XLF)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (P73600_SYNY3 | P73600)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2xlf)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2xlf)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2xlf
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  P73600_SYNY3 | P73600
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  P73600_SYNY3 | P73600
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        P73600_SYNY3 | P73600: 2xl7 2xl9 2xla 2xlg

(-) Related Entries Specified in the PDB File

2xl7 STRUCTURE AND METAL-LOADING OF A SOLUBLE PERIPLASM CUPRO- PROTEIN: CU-CUCA-CLOSED ( SEMET)
2xl9 STRUCTURE AND METAL-LOADING OF A SOLUBLE PERIPLASM CUPRO- PROTEIN: ZN-CUCA-CLOSED ( SEMET)
2xla STRUCTURE AND METAL-LOADING OF A SOLUBLE PERIPLASM CUPRO- PROTEIN: CU-CUCA-CLOSED
2xlg STRUCTURE AND METAL-LOADING OF A SOLUBLE PERIPLASM CUPRO- PROTEIN: CU-CUCA-OPEN