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(-) Description

Title :  CRYSTAL STRUCTURE OF PORB FROM CORYNEBACTERIUM GLUTAMICUM ( CRYSTAL FORM III)
 
Authors :  K. Ziegler, R. Benz, G. E. Schulz
Date :  17 Mar 08  (Deposition) - 20 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.16
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Transmembrane, Membrane Protein, Porin, Membrane, Transport, Ion Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ziegler, R. Benz, G. E. Schulz
A Putative Alpha-Helical Porin From Corynebacterium Glutamicum.
J. Mol. Biol. V. 379 482 2008
PubMed-ID: 18462756  |  Reference-DOI: 10.1016/J.JMB.2008.04.017

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN CGL0972
    Atcc: 13032
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 28-126
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM
    Organism Taxid: 1718
    Synonym: PORB, ANION-SPECIFIC PORIN, ANION-SPECIFIC PORIN PRECURSOR

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
1CAC4Ligand/IonCACODYLATE ION
2ZN12Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CAC2Ligand/IonCACODYLATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CAC2Ligand/IonCACODYLATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CAC-1Ligand/IonCACODYLATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CAC-1Ligand/IonCACODYLATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:68 , GLU B:68BINDING SITE FOR RESIDUE ZN B1089
02AC2SOFTWAREGLU A:46 , ASP B:65 , ASP B:69BINDING SITE FOR RESIDUE ZN B1090
03AC3SOFTWAREGLU A:37 , CAC A:1093 , CAC A:1094 , GLU D:37BINDING SITE FOR RESIDUE ZN A1089
04AC4SOFTWAREGLU A:26 , LYS A:30 , CAC A:1093 , CAC A:1094 , GLU D:26 , LYS D:30BINDING SITE FOR RESIDUE ZN A1090
05AC5SOFTWAREASP A:76 , ASP B:76BINDING SITE FOR RESIDUE ZN A1091
06AC6SOFTWAREASP A:65 , ASP A:69 , GLU B:46BINDING SITE FOR RESIDUE ZN A1092
07AC7SOFTWAREGLU B:26 , LYS B:30 , CAC B:1093 , CAC B:1094 , GLU C:26BINDING SITE FOR RESIDUE ZN B1091
08AC8SOFTWAREGLU B:37 , CAC B:1093 , CAC B:1094 , GLU C:37BINDING SITE FOR RESIDUE ZN B1092
09AC9SOFTWAREASP C:65 , ASP C:69 , GLU D:46BINDING SITE FOR RESIDUE ZN C1089
10BC1SOFTWAREGLU C:68 , GLU D:68BINDING SITE FOR RESIDUE ZN C1090
11BC2SOFTWAREGLU C:46 , ASP D:65 , ASP D:69BINDING SITE FOR RESIDUE ZN D1088
12BC3SOFTWAREASP C:87 , ASP D:76BINDING SITE FOR RESIDUE ZN D1089
13BC4SOFTWAREGLU A:26 , GLU A:37 , LEU A:83 , ZN A:1089 , ZN A:1090 , CAC A:1094 , GLU D:26 , LYS D:30 , GLU D:37BINDING SITE FOR RESIDUE CAC A1093
14BC5SOFTWAREGLU A:26 , LYS A:30 , GLU A:37 , ZN A:1089 , ZN A:1090 , CAC A:1093 , GLU D:26 , GLU D:37 , GLY D:82BINDING SITE FOR RESIDUE CAC A1094
15BC6SOFTWAREGLU B:26 , LYS B:30 , GLU B:37 , ZN B:1091 , ZN B:1092 , CAC B:1094 , GLU C:26 , GLU C:37 , GLY C:82BINDING SITE FOR RESIDUE CAC B1093
16BC7SOFTWAREGLU B:37 , ZN B:1091 , ZN B:1092 , CAC B:1093 , GLU C:26 , GLU C:37BINDING SITE FOR RESIDUE CAC B1094

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:22 -A:81
2B:22 -B:81
3C:22 -C:81
4D:22 -D:81

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VQL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VQL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VQL)

(-) Exons   (0, 0)

(no "Exon" information available for 2VQL)

(-) 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:76
 aligned with Q8NRS3_CORGL | Q8NRS3 from UniProtKB/TrEMBL  Length:126

    Alignment length:76
                                    49        59        69        79        89        99       109      
         Q8NRS3_CORGL    40 LSPQYNWVACGILEGGLKAAGVLEEGQYNRELAEAIAAKGEGFWTTQFPQIGDWNEDQAAALADRAQTCGLVKADT 115
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 2vql A  13 LSPQYNWVACGILEGGLKAAGVLEEGQYNRELAEAIAAKGEGFWTTQFPQIGDWNEDQAAALADRAQTCGLVKADT  88
                                    22        32        42        52        62        72        82      


Chain B from PDB  Type:PROTEIN  Length:73
 aligned with Q8NRS3_CORGL | Q8NRS3 from UniProtKB/TrEMBL  Length:126

    Alignment length:73
                                    52        62        72        82        92       102       112   
         Q8NRS3_CORGL    43 QYNWVACGILEGGLKAAGVLEEGQYNRELAEAIAAKGEGFWTTQFPQIGDWNEDQAAALADRAQTCGLVKADT 115
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 2vql B  16 QYNWVACGILEGGLKAAGVLEEGQYNRELAEAIAAKGEGFWTTQFPQIGDWNEDQAAALADRAQTCGLVKADT  88
                                    25        35        45        55        65        75        85   


Chain C from PDB  Type:PROTEIN  Length:76
 aligned with Q8NRS3_CORGL | Q8NRS3 from UniProtKB/TrEMBL  Length:126

    Alignment length:76
                                    49        59        69        79        89        99       109      
         Q8NRS3_CORGL    40 LSPQYNWVACGILEGGLKAAGVLEEGQYNRELAEAIAAKGEGFWTTQFPQIGDWNEDQAAALADRAQTCGLVKADT 115
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 2vql C  13 LSPQYNWVACGILEGGLKAAGVLEEGQYNRELAEAIAAKGEGFWTTQFPQIGDWNEDQAAALADRAQTCGLVKADT  88
                                    22        32        42        52        62        72        82      


Chain D from PDB  Type:PROTEIN  Length:71
 aligned with Q8NRS3_CORGL | Q8NRS3 from UniProtKB/TrEMBL  Length:126

    Alignment length:71
                                    53        63        73        83        93       103       113 
         Q8NRS3_CORGL    44 YNWVACGILEGGLKAAGVLEEGQYNRELAEAIAAKGEGFWTTQFPQIGDWNEDQAAALADRAQTCGLVKAD 114
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
           Pfam domains (1) PorB-2vqlD01 D:17-87                                                    Pfam domains (1)
           Pfam domains (2) PorB-2vqlD02 D:17-87                                                    Pfam domains (2)
           Pfam domains (3) PorB-2vqlD03 D:17-87                                                    Pfam domains (3)
           Pfam domains (4) PorB-2vqlD04 D:17-87                                                    Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 2vql D  17 YNWVACGILEGGLKAAGVLEEGQYNRELAEAIAAKGEGFWTTQFPQIGDWNEDQAAALADRAQTCGLVKAD  87
                                    26        36        46        56        66        76        86
   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  (0, 0)

(no "SCOP Domain" information available for 2VQL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VQL)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: PorB] (4)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8NRS3_CORGL | Q8NRS3)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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        Q8NRS3_CORGL | Q8NRS3: 2vqg 2vqh 2vqk

(-) Related Entries Specified in the PDB File

2vqg CRYSTAL STRUCTURE OF PORB FROM CORYNEBACTERIUM GLUTAMICUM (CRYSTAL FORM I)
2vqh CRYSTAL STRUCTURE OF PORB FROM CORYNEBACTERIUM GLUTAMICUM (CRYSTAL FORM II)
2vqk CRYSTAL STRUCTURE OF PORB FROM CORYNEBACTERIUM GLUTAMICUM (CRYSTAL FORM IV)