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(-) Description

Title :  CRYSTAL STRUCTURE OF NIKA FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH NI(L-HIS)2 (CO-CRYSTALLIZATION WITH NI(II) AND BHI MEDIUM SUPERNATANT)
 
Authors :  H. Lebrette, C. Cavazza
Date :  12 Jan 15  (Deposition) - 11 Feb 15  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Extracytoplasmic Nickel-Binding Protein, Nickel Import, Abc-Type Importer, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Lebrette, E. Borezee-Durant, L. Martin, P. Richaud, E. Boeri Erba C. Cavazza
Novel Insights Into Nickel Import In Staphylococcus Aureus: The Positive Role Of Free Histidine And Structural Characterization Of A New Thiazolidine-Type Nickel Chelator
Metallomics V. 7 613 2015
PubMed-ID: 25611161  |  Reference-DOI: 10.1039/C4MT00295D

(-) Compounds

Molecule 1 - NICKEL ABC TRANSPORTER SUBSTRATE-BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 19-491
    Gene: AZ30_01190
    Organism Scientific: STAPHYLOCOCCUS AUREUS USA300-ISMMS1
    Organism Taxid: 1458279

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2GOL9Ligand/IonGLYCEROL
3HIS2Mod. Amino AcidHISTIDINE
4NI1Ligand/IonNICKEL (II) ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:502 , HIS A:503binding site for residue NI A 501
02AC2SOFTWARELEU A:17 , ARG A:234 , TYR A:322 , ARG A:325 , ILE A:354 , GLU A:355 , TYR A:369 , SER A:370 , NI A:501 , HIS A:503 , HOH A:777binding site for residue HIS A 502
03AC3SOFTWAREPHE A:134 , ARG A:234 , GLU A:355 , SER A:370 , PHE A:371 , GLY A:372 , ILE A:393 , NI A:501 , HIS A:502 , HOH A:896 , HOH A:907 , HOH A:1003binding site for residue HIS A 503
04AC4SOFTWARELYS A:54 , LYS A:69 , ASP A:70 , ASN A:402binding site for residue GOL A 504
05AC5SOFTWAREGLU A:83 , ALA A:110 , GLN A:295 , ASP A:338 , LYS A:341 , HOH A:645 , HOH A:662binding site for residue GOL A 505
06AC6SOFTWAREILE A:48 , GLU A:49 , LYS A:50 , TYR A:56 , TYR A:101 , ASP A:390 , HOH A:630binding site for residue EPE A 506
07AC7SOFTWAREASP A:256 , ARG A:261 , THR A:277 , PRO A:290 , LYS A:291 , THR A:293 , SER A:431 , HOH A:733 , HOH A:744binding site for residue GOL A 507
08AC8SOFTWARELYS A:32 , LYS A:456 , GLY A:461 , ILE A:462 , TYR A:463 , HOH A:767 , HOH A:862 , HOH A:948 , HOH A:951binding site for residue GOL A 508
09AC9SOFTWAREASP A:260 , GLY A:263 , HIS A:267 , VAL A:334 , HOH A:612 , HOH A:740binding site for residue GOL A 509
10AD1SOFTWARETHR A:109 , ALA A:110 , LYS A:114 , LEU A:115 , THR A:116 , LYS A:245binding site for residue GOL A 510
11AD2SOFTWARELYS A:318 , LYS A:349 , TYR A:357 , HOH A:602binding site for residue GOL A 511
12AD3SOFTWARELYS A:226 , LYS A:453 , ASN A:454 , TYR A:455binding site for residue GOL A 512
13AD4SOFTWARELYS A:143 , LYS A:349 , VAL A:351 , ASP A:352 , ASP A:353 , HOH A:607 , HOH A:897binding site for residue GOL A 513

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XKP)

(-) Sequences/Alignments

Asymmetric/Biological 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:467
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee............hhhhhh......eee.....eee..eeeeeeee..eeeeee............hhhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeee......hhhhhhhhhhhh...................eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....ee...hhhhhhhhhh...eeeeee...eeeeeee.......hhhhhhhhhhhhhhhhhhhhh....eee....................hhhhhhhhhhhh.......eeeeeee.....hhhhhhhhhhhhhhh..eeeeeee..hhhhhhh......eeeeeee......hhhhhhhhh............hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.eeeeeee.eeeeee..ee................ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xkp A   8 GKDLNISLPLKTKSIAPYETDVPVKIGAAESLFKTNDQGKIEKALVKSYHQPNDTTLDIELKDNIKFQNGQKLTAEKVKSSLENSMKKSDLVKYSLPISSITAKGQKLTIKTNSAYPELVSELANPFMAIYDTDAKSDVNQTPVGTGPYQIKDYKQSRKISLSNFKDYWQGKPKLDHITVTYQEDGNNRVRNLESQKDDLITDVPVNKVQDIENNQNLKVSKESGFRTSLLMYNHTNKKMTKSVREALDHIIDRQGIADHIYQGYAKPATSPFNDKIPYIKEPKLTKQNIEQAKMLLAKDGYTKEHPLKIKLITYDGRPELSKIAQVLQSDAKKANIEIDIKSVDDIEGYLKDRSAWDATMYSFGTIPRGDTGYFFNQAYKKDGAINKGDYNNSNVDDLINQLNHTVDVKERHNISNDIIKLSSRDVPNSYIAYNDQIVAANSKVKNYKVTPEGIYLIDYRTTIEHH 503
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467    || 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          472| 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           502
   Legend:   → Mismatch (orange background)
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  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 4XKP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4XKP)

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 Related Entries

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

UniProtKB/TrEMBL
        A0A0J9X272_S | A0A0J9X272: 4xkn 4xkq 4xkr

(-) Related Entries Specified in the PDB File

4ofj THE SAME PROTEIN CO-PURIFIED WITH NI(L-HIS)2
4xkn THE SAME PROTEIN, CO-CRYSTALLIZATION WITH NI(II) AND L-HISTIDINE
4xkq THE SAME PROTEIN, CO-CRYSTALLIZATION WITH NI(II) AND CD MEDIUM SUPERNATANT
4xkr THE SAME PROTEIN, CO-CRYSTALLIZATION WITH NI(II) AND CDDELTAHIS MEDIUM SUPERNATANT