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(-) Description

Title :  X-RAY STRUCTURE OF THE FE(II) FORM OF THE IRON SUPEROXIDE DISMUTASE FROM PSEUDOALTEROMONAS HALOPLANKTIS
 
Authors :  I. Russo Krauss, A. Merlino, F. Sica
Date :  04 Jun 13  (Deposition) - 26 Feb 14  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Superoxide Dismutase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Merlino, I. Russo Krauss, I. Castellano, M. R. Ruocco, A. Capasso, E. De Vendittis, B. Rossi, F. Sica
Structural And Denaturation Studies Of Two Mutants Of A Col Adapted Superoxide Dismutase Point To The Importance Of Electrostatic Interactions In Protein Stability.
Biochim. Biophys. Acta V. 1844 632 2014
PubMed-ID: 24440460  |  Reference-DOI: 10.1016/J.BBAPAP.2014.01.007

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE [FE]
    Chains: A, C, B, D
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SODB, PSHAA1215
    Organism Scientific: PSEUDOALTEROMONAS HALOPLANKTIS
    Organism Taxid: 228

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1FE24Ligand/IonFE (II) ION
2TRE4Ligand/IonTREHALOSE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1FE22Ligand/IonFE (II) ION
2TRE2Ligand/IonTREHALOSE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1FE22Ligand/IonFE (II) ION
2TRE2Ligand/IonTREHALOSE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:26 , HIS A:73 , ASP A:157 , HIS A:161 , HOH A:302BINDING SITE FOR RESIDUE FE2 A 201
2AC2SOFTWAREASN A:116 , ASN A:117 , PHE A:118 , ASN A:137 , SER A:139 , HOH A:338 , HOH A:380 , HOH A:384 , HOH A:392 , HOH A:397 , HOH A:400 , HOH A:422 , GLY B:61 , GLY B:62 , ASN B:65BINDING SITE FOR RESIDUE TRE A 202
3AC3SOFTWAREHIS C:26 , HIS C:73 , ASP C:157 , HIS C:161 , HOH C:327BINDING SITE FOR RESIDUE FE2 C 201
4AC4SOFTWAREASN C:116 , ASN C:117 , PHE C:118 , ASN C:137 , SER C:139 , HOH C:320 , HOH C:325 , HOH C:386 , HOH C:409 , HOH C:433 , GLY D:61 , GLY D:62 , ASN D:65BINDING SITE FOR RESIDUE TRE C 202
5AC5SOFTWAREHIS B:26 , HIS B:73 , ASP B:157 , HIS B:161 , HOH B:302BINDING SITE FOR RESIDUE FE2 B 201
6AC6SOFTWAREGLY A:61 , GLY A:62 , ASN A:65 , HOH A:350 , ASN B:116 , ASN B:117 , PHE B:118 , ASN B:137 , SER B:139 , HOH B:352 , HOH B:364 , HOH B:375 , HOH B:395 , HOH B:397 , HOH B:409 , HOH B:426BINDING SITE FOR RESIDUE TRE B 202
7AC7SOFTWAREHIS D:26 , HIS D:73 , ASP D:157 , HIS D:161 , HOH D:302BINDING SITE FOR RESIDUE FE2 D 201
8AC8SOFTWAREGLY C:61 , GLY C:62 , ASN D:116 , ASN D:117 , PHE D:118 , ASN D:137 , SER D:139 , HOH D:308 , HOH D:364 , HOH D:391 , HOH D:392 , HOH D:417BINDING SITE FOR RESIDUE TRE D 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4L2D)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:15 -Pro A:16
2Glu C:15 -Pro C:16
3Glu B:15 -Pro B:16
4Glu D:15 -Pro D:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L2D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L2D)

(-) Exons   (0, 0)

(no "Exon" information available for 4L2D)

(-) 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:192
                                                                                                                                                                                                                                
               SCOP domains d4l2da1 A:1-82 automated matches                                                  d4l2da2 A:83-192 automated matches                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4l2d A   1 AFELPSLPYAIDALEPHISKETLEFHHGKHHNTYVVKLNGLIPGTKFENKSLEEIVCSSDGGVFNNAAQIWNHTFYWNSLSPNGGGAPTGAVADAINAKWGSFDAFKEALNDKAVNNFGSSWTWLVKLADGSLDIVNTSNAATPLTDDGVTPILTVDLWEHAYYIDYRNVRPDYLKGFWSLVNWEFANANFA 192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  


Chain B from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains d4l2db1 B:1-82 automated matches                                                  d4l2db2 B:83-192 automated matches                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4l2d B   1 AFELPSLPYAIDALEPHISKETLEFHHGKHHNTYVVKLNGLIPGTKFENKSLEEIVCSSDGGVFNNAAQIWNHTFYWNSLSPNGGGAPTGAVADAINAKWGSFDAFKEALNDKAVNNFGSSWTWLVKLADGSLDIVNTSNAATPLTDDGVTPILTVDLWEHAYYIDYRNVRPDYLKGFWSLVNWEFANANFA 192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  


Chain C from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains d4l2dc1 C:1-82 automated matches                                                  d4l2dc2 C:83-192 automated matches                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4l2d C   1 AFELPSLPYAIDALEPHISKETLEFHHGKHHNTYVVKLNGLIPGTKFENKSLEEIVCSSDGGVFNNAAQIWNHTFYWNSLSPNGGGAPTGAVADAINAKWGSFDAFKEALNDKAVNNFGSSWTWLVKLADGSLDIVNTSNAATPLTDDGVTPILTVDLWEHAYYIDYRNVRPDYLKGFWSLVNWEFANANFA 192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  


Chain D from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains d4l2dd1 D:1-82 automated matches                                                  d4l2dd2 D:83-192 automated matches                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4l2d D   1 AFELPSLPYAIDALEPHISKETLEFHHGKHHNTYVVKLNGLIPGTKFENKSLEEIVCSSDGGVFNNAAQIWNHTFYWNSLSPNGGGAPTGAVADAINAKWGSFDAFKEALNDKAVNNFGSSWTWLVKLADGSLDIVNTSNAATPLTDDGVTPILTVDLWEHAYYIDYRNVRPDYLKGFWSLVNWEFANANFA 192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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  (2, 8)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L2D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L2D)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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  SODF_PSEHT | P84612
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 Related Entries

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

UniProtKB/Swiss-Prot
        SODF_PSEHT | P84612: 3lio 3lj9 3ljf 4l2a 4l2b 4l2c

(-) Related Entries Specified in the PDB File

3lio
3lj9
3ljf
4l2a X-RAY STRUCTURE OF THE C57R MUTANT OF THE IRON SUPEROXIDE DISMUTASE FROM PSEUDOALTEROMONAS HALOPLANKTIS (CRYSTAL FORM II)
4l2b X-RAY STRUCTURE OF THE C57S MUTANT OF THE IRON SUPEROXIDE DISMUTASE FROM PSEUDOALTEROMONAS HALOPLANKTIS
4l2c X-RAY STRUCTURE OF THE C57R MUTANT OF THE IRON SUPEROXIDE DISMUTASE FROM PSEUDOALTEROMONAS HALOPLANKTIS (CRYSTAL FORM I)