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(-) Description

Title :  CRYSTAL STRUCTURE OF A HYPOTHETICAL PEROXIREDOXIN PROTEIN FRM SINORHIZOBIUM MELILOTI
 
Authors :  S. Eswaramoorthy, S. Chamala, B. Evans, R. Foti, A. Gizzi, B. Hillerich J. Lafleur, R. Seidel, G. Villigas, W. Zencheck, S. C. Almo, S. Swamina York Structural Genomics Research Consortium (Nysgrc)
Date :  12 Nov 11  (Deposition) - 23 Nov 11  (Release) - 23 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  A  (2x)
Biol. Unit 5:  B,C  (1x)
Keywords :  Nysgrc, Psi Biology, Structural Genomics, New York Structural Genomics Research Consortium, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Eswaramoorthy, S. C. Almo, S. Swaminathan
Crystal Structure Of A Hypothetical Peroxiredoxin Protein From Sinorhizobium Meliloti
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PEROXIREDOXIN PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: R00915, SMC00072
    Organism Scientific: SINORHIZOBIUM MELILOTI
    Organism Taxid: 382

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C
Biological Unit 4 (2x): A  
Biological Unit 5 (1x):  BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric Unit (2, 21)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (2, 8)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION
Biological Unit 4 (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
2SO4-1Ligand/IonSULFATE ION
Biological Unit 5 (2, 14)
No.NameCountTypeFull Name
1MSE13Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:148 , SER B:145 , MSE C:1 , THR C:2BINDING SITE FOR RESIDUE SO4 C 162

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UMA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3UMA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UMA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UMA)

(-) Exons   (0, 0)

(no "Exon" information available for 3UMA)

(-) 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:166
 aligned with Q92RF9_RHIME | Q92RF9 from UniProtKB/TrEMBL  Length:161

    Alignment length:166
                                 1                                                                                                                                                                
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155      
         Q92RF9_RHIME     - -----MTIAVGDKLPNATFKEKTADGPVEVTTELLFKGKRVVLFAVPGAFTPTCSLNHLPGYLENRDAILARGVDDIAVVAVNDLHVMGAWATHSGGMGKIHFLSDWNAAFTKAIGMEIDLSAGTLGIRSKRYSMLVEDGVVKALNIEESPGQATASGAAAMLELL 161
               SCOP domains d3umaa_ A: automated matches                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeee..eeeeeehhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhh......eeee...hhhhhhh..eee.hhhh..eee..eeeeee..eeeeeee..........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uma A  -4 YFQSmmTIAVGDKLPNATFKEKTADGPVEVTTELLFKGKRVVLFAVPGAFTPTCSLNHLPGYLENRDAILARGVDDIAVVAVNDLHVmGAWATHSGGmGKIHFLSDWNAAFTKAIGmEIDLSAGTLGIRSKRYSmLVEDGVVKALNIEESPGQATASGAAAmLELL 161
                                ||   5        15        25        35        45        55        65        75       |85       |95       105      |115       125    |  135       145       155 |    
                                ||                                                                                83-MSE    93-MSE            112-MSE           130-MSE                    157-MSE
                                0-MSE                                                                                                                                                             
                                 1-MSE                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:161
 aligned with Q92RF9_RHIME | Q92RF9 from UniProtKB/TrEMBL  Length:161

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
         Q92RF9_RHIME     1 MTIAVGDKLPNATFKEKTADGPVEVTTELLFKGKRVVLFAVPGAFTPTCSLNHLPGYLENRDAILARGVDDIAVVAVNDLHVMGAWATHSGGMGKIHFLSDWNAAFTKAIGMEIDLSAGTLGIRSKRYSMLVEDGVVKALNIEESPGQATASGAAAMLELL 161
               SCOP domains d3umab_ B: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee..eeeeeehhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhh......eeee...hhhhhhh..eee.hhhh..eee..eeeeee..eeeeeee..........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uma B   1 mTIAVGDKLPNATFKEKTADGPVEVTTELLFKGKRVVLFAVPGAFTPTCSLNHLPGYLENRDAILARGVDDIAVVAVNDLHVmGAWATHSGGmGKIHFLSDWNAAFTKAIGmEIDLSAGTLGIRSKRYSmLVEDGVVKALNIEESPGQATASGAAAmLELL 161
                            |       10        20        30        40        50        60        70        80  |     90  |    100       110 |     120       130       140       150      |160 
                            |                                                                                83-MSE    93-MSE            112-MSE           130-MSE                    157-MSE
                            1-MSE                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:168
 aligned with Q92RF9_RHIME | Q92RF9 from UniProtKB/TrEMBL  Length:161

    Alignment length:168
                                   1                                                                                                                                                                
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153        
         Q92RF9_RHIME     - -------MTIAVGDKLPNATFKEKTADGPVEVTTELLFKGKRVVLFAVPGAFTPTCSLNHLPGYLENRDAILARGVDDIAVVAVNDLHVMGAWATHSGGMGKIHFLSDWNAAFTKAIGMEIDLSAGTLGIRSKRYSMLVEDGVVKALNIEESPGQATASGAAAMLELL 161
               SCOP domains d3umac_ C: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...................eeeeee..eeeeeehhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhh......eeee...hhhhhhh..eee.hhhh..eee..eeeeee..eeeeeee..........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3uma C  -6 NLYFQSmmTIAVGDKLPNATFKEKTADGPVEVTTELLFKGKRVVLFAVPGAFTPTCSLNHLPGYLENRDAILARGVDDIAVVAVNDLHVmGAWATHSGGmGKIHFLSDWNAAFTKAIGmEIDLSAGTLGIRSKRYSmLVEDGVVKALNIEESPGQATASGAAAmLELL 161
                                  || 3        13        23        33        43        53        63        73        83        93       103       113       123      |133       143       153   |    
                                  0-MSE                                                                             83-MSE    93-MSE            112-MSE           130-MSE                    157-MSE
                                   1-MSE
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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  (1, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UMA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UMA)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q92RF9_RHIME | Q92RF9)
molecular function
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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