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(-) Description

Title :  THE 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE PERIPLASMIC DIVALENT CATION TOLERANCE PROTEIN CUTA FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  B. Bagautdinov, T. H. Tahirov, Riken Structural Genomics/Proteomi Initiative (Rsgi)
Date :  11 Dec 13  (Deposition) - 01 Jan 14  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Copper Tolerance, Cuta, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Bagautdinov
The Structures Of The Cuta1 Proteins From Thermus Thermophilus And Pyrococcus Horikoshii: Characterization Of Metal-Binding Sites And Metal-Induced Assembly
Acta Crystallogr. , Sect. F V. 70 404 2014
PubMed-ID: 24699729  |  Reference-DOI: 10.1107/S2053230X14003422

(-) Compounds

Molecule 1 - DIVALENT-CATION TOLERANCE PROTEIN CUTA
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CUTA, PH0992
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 22)

Asymmetric Unit (5, 22)
No.NameCountTypeFull Name
1CL8Ligand/IonCHLORIDE ION
2CSD6Mod. Amino Acid3-SULFINOALANINE
3MES4Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4NA2Ligand/IonSODIUM ION
5SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CSD3Mod. Amino Acid3-SULFINOALANINE
3MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4NA-1Ligand/IonSODIUM ION
5SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CSD3Mod. Amino Acid3-SULFINOALANINE
3MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4NA-1Ligand/IonSODIUM ION
5SO41Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:307 , HOH A:335 , HOH B:308 , HOH B:314 , HOH C:310 , HOH C:329BINDING SITE FOR RESIDUE NA A 201
02AC2SOFTWAREARG A:33 , ARG B:33 , ARG C:33BINDING SITE FOR RESIDUE CL A 202
03AC3SOFTWARETYR A:39 , TRP A:41 , TYR A:75 , ASP A:76 , VAL A:77 , TYR B:92 , TRP B:95BINDING SITE FOR RESIDUE MES A 203
04AC4SOFTWARELYS B:70 , HOH B:336 , ASN C:89 , GLU C:90 , GLU F:59 , ASP F:60BINDING SITE FOR RESIDUE CL B 201
05AC5SOFTWAREMET B:1 , GLU B:59BINDING SITE FOR RESIDUE CL B 202
06AC6SOFTWARETYR B:39 , TRP B:41 , TYR B:75 , ASP B:76 , VAL B:77 , TYR C:92BINDING SITE FOR RESIDUE MES B 203
07AC7SOFTWAREASN A:89 , GLU A:90 , LYS C:66 , LYS C:70BINDING SITE FOR RESIDUE CL C 201
08AC8SOFTWARELYS B:23 , TYR C:75 , ASP C:76 , VAL C:77 , HOH C:379BINDING SITE FOR RESIDUE SO4 C 202
09AC9SOFTWAREHOH D:3138 , HOH D:3142 , HOH E:4115 , HOH E:4144 , HOH F:307 , HOH F:375BINDING SITE FOR RESIDUE NA D 3001
10BC1SOFTWARELYS D:66 , LYS D:70 , ASN E:89 , GLU E:90BINDING SITE FOR RESIDUE CL D 3002
11BC2SOFTWAREASN D:89 , GLU D:90 , LYS F:66 , LYS F:70BINDING SITE FOR RESIDUE CL D 3003
12BC3SOFTWAREMET D:1 , GLU D:59 , HOH D:3132BINDING SITE FOR RESIDUE CL D 3004
13BC4SOFTWAREARG D:33 , ILE D:54 , ARG E:33 , ILE E:54 , ARG F:33 , ILE F:54BINDING SITE FOR RESIDUE SO4 D 3005
14BC5SOFTWARETRP D:41 , TYR D:75 , ASP D:76 , VAL D:77 , HOH D:3224 , TYR E:92BINDING SITE FOR RESIDUE MES D 3006
15BC6SOFTWARELYS E:66 , LYS E:70 , ASN F:89 , GLU F:90BINDING SITE FOR RESIDUE CL E 4001
16BC7SOFTWARETYR D:92 , TRP F:41 , TYR F:75 , ASP F:76 , VAL F:77BINDING SITE FOR RESIDUE MES F 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NYO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NYO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NYO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NYO)

(-) Exons   (0, 0)

(no "Exon" information available for 4NYO)

(-) 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:102
                                                                                                                                      
               SCOP domains d4nyoa_ A: Cut A1                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhh....................eeeeeeeeeeeeehhhhhhhhhhhhhhhh.......eeee..eehhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4nyo A   1 MIIVYTTFPDWESAEKVVKTLLKERLIAcANLREHRAFYWWEGKIEEDKEVGAILKTREDLWEELKERIKELHPYDVPAIIRIDVDDVNEDYLKWLIEETKK 102
                                    10        20        30        40        50        60        70        80        90       100  
                                                       29-CSD                                                                     


Chain B from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               SCOP domains d4nyob_ B: Cut A1                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhh...................eeeeeeeeeeeeeehhhhhhhhhhhhhhhh.......eeee..eehhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4nyo B   1 MIIVYTTFPDWESAEKVVKTLLKERLIAcANLREHRAFYWWEGKIEEDKEVGAILKTREDLWEELKERIKELHPYDVPAIIRIDVDDVNEDYLKWLIEETKK 102
                                    10        20        30        40        50        60        70        80        90       100  
                                                       29-CSD                                                                     


Chain C from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               SCOP domains d4nyoc_ C: Cut A1                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhh...................eeeeeeeeeeeeeehhhhhhhhhhhhhhhh.......eeee..eehhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4nyo C   1 MIIVYTTFPDWESAEKVVKTLLKERLIAcANLREHRAFYWWEGKIEEDKEVGAILKTREDLWEELKERIKELHPYDVPAIIRIDVDDVNEDYLKWLIEETKK 102
                                    10        20        30        40        50        60        70        80        90       100  
                                                       29-CSD                                                                     


Chain D from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               SCOP domains d4nyod_ D: Cut A1                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhh...................eeeeeeeeeeeeeehhhhhhhhhhhhhhhh.......eeee..eehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4nyo D   1 MIIVYTTFPDWESAEKVVKTLLKERLIAcANLREHRAFYWWEGKIEEDKEVGAILKTREDLWEELKERIKELHPYDVPAIIRIDVDDVNEDYLKWLIEETKK 102
                                    10        20        30        40        50        60        70        80        90       100  
                                                       29-CSD                                                                     


Chain E from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               SCOP domains d4nyoe_ E: Cut A1                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhh...................eeeeeeeeeeeeeehhhhhhhhhhhhhhhh.......eeee..eehhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4nyo E   1 MIIVYTTFPDWESAEKVVKTLLKERLIAcANLREHRAFYWWEGKIEEDKEVGAILKTREDLWEELKERIKELHPYDVPAIIRIDVDDVNEDYLKWLIEETKK 102
                                    10        20        30        40        50        60        70        80        90       100  
                                                       29-CSD                                                                     


Chain F from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               SCOP domains d4nyof_ F: Cut A1                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhh...................eeeeeeeeeeeeeehhhhhhhhhhhhhhhh.......eeee..eehhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4nyo F   1 MIIVYTTFPDWESAEKVVKTLLKERLIAcANLREHRAFYWWEGKIEEDKEVGAILKTREDLWEELKERIKELHPYDVPAIIRIDVDDVNEDYLKWLIEETKK 102
                                    10        20        30        40        50        60        70        80        90       100  
                                                       29-CSD
   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  (1, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NYO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NYO)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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  CUTA_PYRHO | O58720
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 Related Entries

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        CUTA_PYRHO | O58720: 1j2v 1uku 1umj 2e66 4nyp

(-) Related Entries Specified in the PDB File

4nyp RELATED ID: RSGI-PHO001000992.2 RELATED DB: TARGETTRACK