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(-) Description

Title :  CROSS-LINKED BARNASE SOAKED IN BROMO-ETHANOL
 
Authors :  T. Prange, M. Salem
Date :  26 Nov 05  (Deposition) - 25 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Denaturation, Lysozyme, Barnase, Cross-Linked Crystals, Glutaraldehyde, Urea, Thiourea, Bromoethanol, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Salem, Y. Mauguen, T. Prange
On The Edge Of The Denaturation Process: Application Of X-Ray Diffraction To Barnase And Lysozyme Cross-Linked Crystals With Denaturants In Molar Concentrations.
Biochim. Biophys. Acta V. 1764 903 2006
PubMed-ID: 16600702  |  Reference-DOI: 10.1016/J.BBAPAP.2006.02.009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE
    ChainsA, B, C
    EC Number3.1.27.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMJ1002
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificBACILLUS AMYLOLIQUEFACIENS
    Organism Taxid1390
    SynonymBARNASE, RNASE BA

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1BRJ2Ligand/Ion2-BROMOETHANOL
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1BRJ-1Ligand/Ion2-BROMOETHANOL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1BRJ2Ligand/Ion2-BROMOETHANOL
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1BRJ-1Ligand/Ion2-BROMOETHANOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:80 , LYS A:106 , LYS B:37 , ASN B:39 , ASP B:42BINDING SITE FOR RESIDUE BRJ B 150
2AC2SOFTWAREPHE B:80 , LYS B:106 , ARG B:108 , LEU C:31 , VAL C:43 , ALA C:44BINDING SITE FOR RESIDUE BRJ B 151

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F5M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2F5M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F5M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F5M)

(-) Exons   (0, 0)

(no "Exon" information available for 2F5M)

(-) 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:108
 aligned with RNBR_BACAM | P00648 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:108
                                    59        69        79        89        99       109       119       129       139       149        
           RNBR_BACAM    50 VINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 157
               SCOP domains d2f5ma_ A: Barnase                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.....eehhhhhhhh..hhhhhhhhhhh...eeeeeee..............eeeee...........eeeee....eeee.......eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2f5m A   1 VINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 108
                                    10        20        30        40        50        60        70        80        90       100        

Chain B from PDB  Type:PROTEIN  Length:108
 aligned with RNBR_BACAM | P00648 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:108
                                    59        69        79        89        99       109       119       129       139       149        
           RNBR_BACAM    50 VINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 157
               SCOP domains d2f5mb_ B: Barnase                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.....eehhhhhhhh..hhhhhhhhhhh...eeeeeee..............eeeee...........eeeee....eeee.......ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2f5m B   1 VINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 108
                                    10        20        30        40        50        60        70        80        90       100        

Chain C from PDB  Type:PROTEIN  Length:108
 aligned with RNBR_BACAM | P00648 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:108
                                    59        69        79        89        99       109       119       129       139       149        
           RNBR_BACAM    50 VINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 157
               SCOP domains d2f5mc_ C: Barnase                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.....eehhhhhhhh..hhhhhhhhhhh...eeeeeee..............eeeee...........eeeee....eeee.......eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2f5m C   1 VINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 108
                                    10        20        30        40        50        60        70        80        90       100        

   Legend:   → Mismatch (orange background)
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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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2F5M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F5M)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (RNBR_BACAM | P00648)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RNBR_BACAM | P006481a2p 1b20 1b21 1b27 1b2s 1b2u 1b2x 1b2z 1b3s 1ban 1bao 1bgs 1bne 1bnf 1bng 1bni 1bnj 1bnr 1bns 1brg 1brh 1bri 1brj 1brk 1brn 1brs 1bsa 1bsb 1bsc 1bsd 1bse 1fw7 1rnb 1x1u 1x1w 1x1x 1x1y 1yvs 2c4b 2f4y 2f56 2f5w 2kf3 2kf4 2kf5 2kf6 2za4 3da7 3kch 3q3f

(-) Related Entries Specified in the PDB File

2f4y 2f56