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(-) Description

Title :  CRYSTAL STRUCTURE OF NIKA FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH NI-(L-HIS)(2-METHYL-THIAZOLIDINE DICARBOXYLATE) (CO-CRYSTALLIZATION WITH NI(II) AND CDDELTAHIS 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 :  1.75
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  (6, 23)

Asymmetric/Biological Unit (6, 23)
No.NameCountTypeFull Name
141K1Ligand/Ion(2R,4R)-2-METHYL-1,3-THIAZOLIDINE-2,4-DICARBOXYLIC ACID
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3GOL18Ligand/IonGLYCEROL
4HIS1Mod. Amino AcidHISTIDINE
5NA1Ligand/IonSODIUM ION
6NI1Ligand/IonNICKEL (II) ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:502 , 41K A:503binding site for residue NI A 501
02AC2SOFTWARELEU A:17 , ARG A:234 , TYR A:322 , ARG A:325 , GLU A:355 , TYR A:369 , SER A:370 , NI A:501 , 41K A:503 , NA A:523 , HOH A:773binding site for residue HIS A 502
03AC3SOFTWAREASP A:28 , PHE A:134 , ARG A:234 , TYR A:369 , SER A:370 , PHE A:371 , GLY A:372 , ILE A:393 , NI A:501 , HIS A:502 , NA A:523 , HOH A:752 , HOH A:784 , HOH A:836 , HOH A:846binding site for residue 41K A 503
04AC4SOFTWAREILE A:48 , GLU A:49 , LYS A:50 , TYR A:56 , TYR A:101 , LYS A:389 , ASP A:390 , ASP A:404 , GOL A:508 , HOH A:645 , HOH A:676 , HOH A:961binding site for residue EPE A 504
05AC5SOFTWARELYS A:159 , LYS A:318 , LYS A:349 , TYR A:357 , HOH A:610 , HOH A:986binding site for residue GOL A 505
06AC6SOFTWARELYS A:32 , LYS A:456 , GLY A:461 , ILE A:462 , TYR A:463 , HOH A:759 , HOH A:786 , HOH A:840 , HOH A:990binding site for residue GOL A 506
07AC7SOFTWAREGLU A:83 , ALA A:110 , GLN A:295 , ILE A:297 , ASP A:338 , GOL A:521 , HOH A:625 , HOH A:644 , HOH A:668binding site for residue GOL A 507
08AC8SOFTWARETYR A:101 , ASN A:384 , LYS A:388 , LYS A:389 , EPE A:504 , HOH A:845binding site for residue GOL A 508
09AC9SOFTWAREASP A:260 , GLY A:263 , ILE A:264 , HIS A:267 , VAL A:334 , HOH A:800 , HOH A:815 , HOH A:1046binding site for residue GOL A 509
10AD1SOFTWAREGLU A:90 , SER A:106 , ILE A:108 , HOH A:673 , HOH A:818binding site for residue GOL A 510
11AD2SOFTWARESER A:55 , GLU A:67 , ARG A:252 , TYR A:398 , ASN A:399 , ASN A:400 , ASP A:433 , GOL A:518 , HOH A:602 , HOH A:612binding site for residue GOL A 511
12AD3SOFTWAREASP A:256 , ARG A:261 , THR A:277 , PRO A:290 , LYS A:291 , THR A:293 , SER A:431 , HOH A:742 , HOH A:772 , HOH A:798binding site for residue GOL A 512
13AD4SOFTWAREGLN A:58 , ASN A:60 , ASP A:61 , THR A:63 , THR A:119 , ALA A:122 , TYR A:123 , HOH A:771binding site for residue GOL A 513
14AD5SOFTWARETHR A:149 , LYS A:159 , ILE A:348 , LYS A:349 , SER A:350 , HOH A:619 , HOH A:666binding site for residue GOL A 514
15AD6SOFTWARETYR A:463 , HOH A:749 , HOH A:826 , HOH A:855 , HOH A:869 , HOH A:889 , HOH A:910binding site for residue GOL A 515
16AD7SOFTWARELYS A:226 , LYS A:453 , ASN A:454 , TYR A:455 , HOH A:1007binding site for residue GOL A 516
17AD8SOFTWARELYS A:143 , VAL A:351 , ASP A:352 , ASP A:353binding site for residue GOL A 517
18AD9SOFTWARELYS A:114 , HIS A:242 , LYS A:245 , MET A:247 , THR A:248 , ARG A:252 , GOL A:511 , HOH A:602 , HOH A:675 , HOH A:681binding site for residue GOL A 518
19AE1SOFTWARELYS A:54 , LYS A:69 , ASP A:70 , ASN A:71 , ASN A:402 , HOH A:632 , HOH A:957binding site for residue GOL A 519
20AE2SOFTWARETHR A:109 , ALA A:110 , LYS A:114 , LEU A:115 , THR A:116 , LYS A:245binding site for residue GOL A 520
21AE3SOFTWAREGLU A:83 , LYS A:86 , THR A:109 , ALA A:110 , GLU A:298 , LYS A:341 , GOL A:507binding site for residue GOL A 521
22AE4SOFTWAREPHE A:134 , ALA A:392 , LYS A:395 , NA A:523 , HOH A:820 , HOH A:893 , HOH A:940 , HOH A:969binding site for residue GOL A 522
23AE5SOFTWAREGLU A:355 , HIS A:502 , 41K A:503 , GOL A:522 , HOH A:813binding site for residue NA A 523

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XKR)

(-) 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:465
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               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...hhhhhhhhhhh..eeeeee...eeeeeee.......hhhhhhhhhhhhhhhhhhhhh....eee....................hhhhhhhhhhh........eeeeeee.....hhhhhhhhhhhhhhhh.eeeeeee..hhhhhhh......eeeeeee......hhhhhhhhh............hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.eeeeeee.eeeeee..ee................ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xkr A   9 KDLNISLPLKTKSIAPYETDVPVKIGAAESLFKTNDQGKIEKALVKSYHQPNDTTLDIELKDNIKFQNGQKLTAEKVKSSLENSMKKSDLVKYSLPISSITAKGQKLTIKTNSAYPELVSELANPFMAIYDTDAKSDVNQTPVGTGPYQIKDYKQSRKISLSNFKDYWQGKPKLDHITVTYQEDGNNRVRNLESQKDDLITDVPVNKVQDIENNQNLKVSKESGFRTSLLMYNHTNKKMTKSVREALDHIIDRQGIADHIYQGYAKPATSPFNDKIPYIKEPKLTKQNIEQAKMLLAKDGYTKEHPLKIKLITYDGRPELSKIAQVLQSDAKKANIEIDIKSVDDIEGYLKDRSAWDATMYSFGTIPRGDTGYFFNQAYKKDGAINKGDYNNSNVDDLINQLNHTVDVKERHNISNDIIKLSSRDVPNSYIAYNDQIVAANSKVKNYKVTPEGIYLIDYRTTIEH 502
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468   ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         472|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          502
   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  (0, 0)

(no "SCOP Domain" information available for 4XKR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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 Related Entries

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

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

(-) 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
4xkp THE SAME PROTEIN, CO-CRYSTALLIZATION WITH NI(II) AND BHI MEDIUM SUPERNATANT
4xkq THE SAME PROTEIN, CO-CRYSTALLIZATION WITH NI(II) AND CD MEDIUM SUPERNATANT