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(-) Description

Title :  THE CRYSTAL STRUCTURE OF HELICOBACTER PYLORI CEUE (HP1561) WITH NI(II) BOUND
 
Authors :  M. M. Shaik, L. Cendron, G. Zanotti
Date :  05 Jan 13  (Deposition) - 08 Jan 14  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Heme-Binding Protein, Fe Transport, Abc Transporter Substrate Binding Protein, Periplasmic Space, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Shaik, L. Cendron, M. Salamina, M. Ruzzene, G. Zanotti
Helicobacter Pylori Periplasmic Receptor Ceue (Hp1561) Modulates Its Nickel Affinity Via Organic Metallophores.
Mol. Microbiol. V. 91 724 2014
PubMed-ID: 24330328  |  Reference-DOI: 10.1111/MMI.12487

(-) Compounds

Molecule 1 - IRON (III) ABC TRANSPORTER, PERIPLASMIC IRON-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET101-HP1561
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 32-333
    Gene: HPG27_1499
    Mutation: YES
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 563041
    Strain: G27
    Synonym: CEUE

 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  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1ACT8Ligand/IonACETATE ION
2NI6Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:103 , HOH A:605 , HOH A:607 , HOH A:609BINDING SITE FOR RESIDUE NI A 401
02AC2SOFTWAREGLU A:153 , ACT A:407 , HOH A:612BINDING SITE FOR RESIDUE NI A 402
03AC3SOFTWAREACT A:405 , ACT A:406 , HOH A:578 , HOH A:611BINDING SITE FOR RESIDUE NI A 403
04AC4SOFTWAREGLN A:144 , ASP A:154 , HOH A:610 , NI B:403BINDING SITE FOR RESIDUE ACT A 404
05AC5SOFTWARENI A:403 , ACT A:406 , GLN B:144 , ASP B:154BINDING SITE FOR RESIDUE ACT A 405
06AC6SOFTWARENI A:403 , ACT A:405 , HOH A:611 , LYS B:39BINDING SITE FOR RESIDUE ACT A 406
07AC7SOFTWAREGLU A:153 , NI A:402BINDING SITE FOR RESIDUE ACT A 407
08AC8SOFTWAREHIS B:103 , ACT B:404 , HOH B:585 , HOH B:586BINDING SITE FOR RESIDUE NI B 401
09AC9SOFTWAREGLU B:153 , ACT B:405 , ACT B:406 , HOH B:584BINDING SITE FOR RESIDUE NI B 402
10BC1SOFTWAREACT A:404 , HOH A:610 , ACT B:407 , HOH B:582 , HOH B:583BINDING SITE FOR RESIDUE NI B 403
11BC2SOFTWAREGLY B:58 , ARG B:230 , TRP B:249 , ILE B:284 , NI B:401 , HOH B:504 , HOH B:585BINDING SITE FOR RESIDUE ACT B 404
12BC3SOFTWAREGLU B:153 , NI B:402BINDING SITE FOR RESIDUE ACT B 405
13BC4SOFTWAREGLU B:153 , NI B:402 , HOH B:584BINDING SITE FOR RESIDUE ACT B 406
14BC5SOFTWAREGLU B:94 , NI B:403 , HOH B:583BINDING SITE FOR RESIDUE ACT B 407

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:49 -Pro A:50
2His A:103 -Ala A:104
3Leu B:49 -Pro B:50
4His B:103 -Ala B:104

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4INP)

(-) 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:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee....eeee......eeee....hhhhhhhhhh.eeeee.hhhhhhhhhhhh.hhhhheee........hhhhhhhhh..eeeee..hhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....eeeeee.....eee...hhhhhhhhhh.eee.hhhh....eee.hhhhhhhhh..eeee......hhhhhhhhhhhh.hhhhhh..eee.........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4inp A  35 EVKVKDYFGEQTIKLPVSKIIYLGSFAEVPAMFHTWDRVVGISDYAFKSDIVKATLKDPERIKPMSSDHAAALNVELLKKLSPDLVVTFVGNPKAVEHAKKFGISFLSFQEKTIAEVMEDIDTQAKALEVDASKKLAKMQETLDFIAERLKGVKKKKGVELFHKANKISGHQALDSDILEKGGIDNFGLKYVKFGRADISVEKIVKENPEIIFIWWISPLSPEDVLNNPKFATIKAIKNKQVYKLPTMDIGGPRAPLISLFIALKAHPEAFKGVDINAIVKDYYKVVFDLNDAEVEPFLW 334
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334


Chain B from PDB  Type:PROTEIN  Length:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee....eeee......eeee....hhhhhhhhhh.eeeee.hhhhhhhhhhhh.hhhhheee........hhhhhhhhh..eeeee..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eeeeee.....eee...hhhhhhhhhh.eee.hhhh....eee.hhhhhhhhh..eeee......hhhhhhhhhhhh.hhhhhh..eee.........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4inp B  35 EVKVKDYFGEQTIKLPVSKIIYLGSFAEVPAMFHTWDRVVGISDYAFKSDIVKATLKDPERIKPMSSDHAAALNVELLKKLSPDLVVTFVGNPKAVEHAKKFGISFLSFQEKTIAEVMEDIDTQAKALEVDASKKLAKMQETLDFIAERLKGVKKKKGVELFHKANKISGHQALDSDILEKGGIDNFGLKYVKFGRADISVEKIVKENPEIIFIWWISPLSPEDVLNNPKFATIKAIKNKQVYKLPTMDIGGPRAPLISLFIALKAHPEAFKGVDINAIVKDYYKVVFDLNDAEVEPFLW 334
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334
   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 4INP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  Cis Peptide Bonds
    His A:103 - Ala A:104   [ RasMol ]  
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4ino