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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PERIPLASMIC NICKEL-BINDING PROTEIN NIKA FROM ESCHERICHIA COLI IN COMPLEX WITH RU(BPZA)(CO)2CL
 
Authors :  C. Cavazza, S. Lopez, L. Rondot, M. Iannello, E. Boeri-Erba, N. Burzlaf F. Strinitz, A. Jorge-Robin, C. Marchi-Delapierre, S. Menage
Date :  20 Jan 17  (Deposition) - 22 Feb 17  (Release) - 22 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Artificial Metalloenzymes, Chlorine Insertion, Chlorhydrins, Bio- Inspired Chemistry, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Lopez, L. Rondot, C. Cavazza, M. Iannello, E. Boeri-Erba, N. Burzlaff, N. Strinitz, A. Jorge-Robin, C. Marchi-Delapierre, S. Menage
Efficient Conversion Of Alkenes To Chlorohydrins By A Ru-Based Artificial Enzyme
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NICKEL-BINDING PERIPLASMIC PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: NIKA, B3476, JW3441
    Organism Scientific: ESCHERICHIA COLI K12
    Organism Taxid: 83333

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 31)

Asymmetric Unit (9, 31)
No.NameCountTypeFull Name
16RP1Ligand/IonBIS(PYRZOL-1-YL)ACETATE SCORPIONATE
2ACT10Ligand/IonACETATE ION
3CL2Ligand/IonCHLORIDE ION
4CMO2Ligand/IonCARBON MONOXIDE
5EDT1Ligand/Ion{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID
6FE1Ligand/IonFE (III) ION
7GOL12Ligand/IonGLYCEROL
8RU1Ligand/IonRUTHENIUM ION
9SO41Ligand/IonSULFATE ION
Biological Unit 1 (4, 16)
No.NameCountTypeFull Name
16RP-1Ligand/IonBIS(PYRZOL-1-YL)ACETATE SCORPIONATE
2ACT7Ligand/IonACETATE ION
3CL-1Ligand/IonCHLORIDE ION
4CMO-1Ligand/IonCARBON MONOXIDE
5EDT1Ligand/Ion{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID
6FE-1Ligand/IonFE (III) ION
7GOL7Ligand/IonGLYCEROL
8RU-1Ligand/IonRUTHENIUM ION
9SO41Ligand/IonSULFATE ION
Biological Unit 2 (4, 11)
No.NameCountTypeFull Name
16RP1Ligand/IonBIS(PYRZOL-1-YL)ACETATE SCORPIONATE
2ACT3Ligand/IonACETATE ION
3CL-1Ligand/IonCHLORIDE ION
4CMO2Ligand/IonCARBON MONOXIDE
5EDT-1Ligand/Ion{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID
6FE-1Ligand/IonFE (III) ION
7GOL5Ligand/IonGLYCEROL
8RU-1Ligand/IonRUTHENIUM ION
9SO4-1Ligand/IonSULFATE ION

(-) Sites  (31, 31)

Asymmetric Unit (31, 31)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:68 , ASP A:69 , ASP A:70binding site for residue ACT A 601
02AC2SOFTWAREASN A:261 , GLU A:262 , LEU A:263 , HOH A:932binding site for residue ACT A 602
03AC3SOFTWAREASN A:235 , ALA A:237 , GLN A:423 , HOH A:799 , HOH A:894binding site for residue ACT A 603
04AC4SOFTWAREARG A:384 , ARG A:389 , HOH A:763 , LEU B:430 , ARG B:457binding site for residue SO4 A 604
05AC5SOFTWAREASN A:220 , GLU A:247 , ARG A:396 , THR A:490 , GOL A:606 , HOH A:709 , HOH A:802 , HOH A:834 , HOH A:915binding site for residue GOL A 605
06AC6SOFTWARETRP A:10 , PRO A:11 , GLY A:219 , ASN A:220 , GLY A:222 , LEU A:223 , GOL A:605 , HOH A:792binding site for residue GOL A 606
07AC7SOFTWAREGLU A:102 , ASN A:105 , LYS A:123 , ASP A:227 , THR A:228 , ARG A:231 , ARG A:412binding site for residue GOL A 607
08AC8SOFTWAREEDT A:609 , HOH A:703binding site for residue FE A 608
09AC9SOFTWARETYR A:22 , MET A:27 , ARG A:97 , TRP A:100 , ARG A:137 , TRP A:398 , FE A:608 , HOH A:703 , HOH A:733 , HOH A:738 , HOH A:834 , HOH A:845 , HOH A:908 , HOH A:923binding site for residue EDT A 609
10AD1SOFTWAREGLN A:361 , SER A:372 , LEU A:373binding site for residue ACT A 610
11AD2SOFTWAREASN A:149 , LYS A:157binding site for residue ACT A 611
12AD3SOFTWARELYS A:335 , HOH A:947 , ARG B:341binding site for residue ACT A 612
13AD4SOFTWAREALA A:158 , LEU A:167 , GLN A:168 , HOH A:759 , THR B:211 , ASP B:213binding site for residue GOL A 613
14AD5SOFTWAREPRO A:327 , ALA A:328 , HOH A:863 , ARG B:365 , GLN B:366binding site for residue GOL A 614
15AD6SOFTWARELYS A:316 , HOH A:737 , LYS B:354binding site for residue GOL A 615
16AD7SOFTWAREARG A:89 , LEU A:92 , ARG A:95 , ILE A:107 , VAL A:108 , ASP A:109 , VAL A:110 , ASN A:281 , HOH A:957binding site for residue GOL A 616
17AD8SOFTWARETHR A:23 , GLN A:26 , HOH A:795 , HOH A:920binding site for residue ACT A 617
18AD9SOFTWAREASN A:75 , GLY A:76 , PRO B:225 , ASP B:227binding site for residue ACT B 601
19AE1SOFTWARESER B:243 , ILE B:246 , TYR B:485 , ALA B:486 , HOH B:703 , HOH B:710 , HOH B:731 , HOH B:743binding site for residue GOL B 602
20AE2SOFTWARETRP B:10 , PRO B:11 , GLY B:219 , ASN B:220 , GLY B:222 , LEU B:223 , GOL B:604 , HOH B:725 , HOH B:884binding site for residue GOL B 603
21AE3SOFTWAREASN B:220 , GLU B:247 , ARG B:396 , ALA B:489 , THR B:490 , GOL B:603 , HOH B:706 , HOH B:709binding site for residue GOL B 604
22AE4SOFTWAREHOH B:866binding site for residue ACT B 605
23AE5SOFTWARECL B:607 , 6RP B:608 , CMO B:609 , CMO B:610binding site for residue RU B 606
24AE6SOFTWARERU B:606 , 6RP B:608 , CMO B:609 , CMO B:610 , HOH B:920 , HOH B:951binding site for residue CL B 607
25AE7SOFTWARETYR B:22 , MET B:27 , TRP B:100 , ARG B:137 , TRP B:398 , TYR B:402 , RU B:606 , CL B:607 , CMO B:609 , CMO B:610 , HOH B:769binding site for residue 6RP B 608
26AE8SOFTWAREARG B:137 , RU B:606 , CL B:607 , 6RP B:608 , CMO B:610binding site for residue CMO B 609
27AE9SOFTWARERU B:606 , CL B:607 , 6RP B:608 , CMO B:609binding site for residue CMO B 610
28AF1SOFTWAREASN B:274 , LYS B:275 , LYS B:276 , SER B:308 , GLN B:309 , TYR B:310 , HOH B:702 , HOH B:859binding site for residue GOL B 611
29AF2SOFTWAREMET B:27 , PHE B:28 , THR B:490 , HOH B:943 , HOH B:976binding site for residue CL B 612
30AF3SOFTWARETHR B:23 , GLN B:26 , HOH B:951binding site for residue ACT B 613
31AF4SOFTWARETHR A:23 , ARG A:97 , LYS B:314 , HOH B:701 , HOH B:707binding site for residue GOL B 614

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5MWU)

(-) Cis Peptide Bonds  (11, 12)

Asymmetric Unit
No.Residues
1Thr A:23 -Pro A:24
2Arg A:137 -Pro A:138
3Ala A:258 -Pro A:259
4Ala A:400 -Pro A:401
5Asp A:403 -Pro A:404
6Thr B:23 -Pro B:24
7Arg B:137 -Pro B:138
8Ala B:258 -Pro B:259
9Ala B:328 -Gly B:329
10Ala B:400 -Pro B:401
11Asp B:403 -Pro B:404

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5MWU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5MWU)

(-) Exons   (0, 0)

(no "Exon" information available for 5MWU)

(-) 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:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee...............hhhhhhhhh...eee.....eee..eeeeee.....eeeeee............hhhhhhhhhhhhhhhhhhhh..hhhhheeeeee....eeeeee.....hhhhhhh........hhh.ee..eeeeee........eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....eeee.....hhhhhhhhhh....eeee....eeeeeee........hhhhhhhhhhhhhhhhhhhhhh....ee.....................hhhhhhhhhhhh...........ee..ee.eeeeeee..hhhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh...eeeee.......hhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeeee..eeee.hhhh...........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5mwu A   2 APDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKP 499
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491        


Chain B from PDB  Type:PROTEIN  Length:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee...............hhhhhhhhh...eee.....eee..eeeeee.....eeeeee............hhhhhhhhhhhhhhhhhhhh.hhhhhheeeeee....eeeeee.....hhhhhhh........hhh.ee..eeeeee........eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....eeee.....hhhhhhhhhh....eeeeeeeeeeeeeee........hhhhhhhhhhhhhhhhhhhhhh....ee.....................hhhhhhhhhhhh..................eeeeeee..hhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhh...eeeee.......hhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee.hhhh...........hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5mwu B   3 PDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKPV 500
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492
   Legend:   → Mismatch (orange background)
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    → 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 5MWU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5MWU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5MWU)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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    Ala B:328 - Gly B:329   [ RasMol ]  
    Ala B:400 - Pro B:401   [ RasMol ]  
    Arg A:137 - Pro A:138   [ RasMol ]  
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  5mwu
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 Related Entries

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UniProtKB/Swiss-Prot
        NIKA_ECOLI | P33590: 1uiu 1uiv 1zlq 2noo 3dp8 3e3k 3mvw 3mvx 3mvy 3mvz 3mw0 3mz9 3mzb 3qim 4dcx 4dcy 4i8c 4i9d 5l8d

(-) Related Entries Specified in the PDB File

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