Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN MUTANTS TO STUDY DETERMINANTS OF PROTEIN STABILITY
 
Authors :  H. Delbrueck, U. Mueller, D. Perl, F. X. Schmid, U. Heinemann
Date :  27 Feb 01  (Deposition) - 07 Nov 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Barrel, Homodimer, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Delbruck, U. Mueller, D. Perl, F. X. Schmid, U. Heinemann
Crystal Structures Of Mutant Forms Of The Bacillus Caldolyticus Cold Shock Protein Differing In Thermal Stability.
J. Mol. Biol. V. 313 359 2001
PubMed-ID: 11800562  |  Reference-DOI: 10.1006/JMBI.2001.5051
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COLD-SHOCK PROTEIN CSPB
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CSPB
    Mutation: YES
    Organism Scientific: BACILLUS CALDOLYTICUS
    Organism Taxid: 1394
    Synonym: CSPB, BC-CSP

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:20 , GLY A:23 , HOH A:950 , HOH A:1019 , HOH A:1096 , HOH A:1135BINDING SITE FOR RESIDUE NA A 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I5F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1I5F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I5F)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COLD_SHOCKPS00352 'Cold-shock' domain signature.CSPB_BACCL15-33
 		  2A:15-33
B:15-33

(-) Exons   (0, 0)

(no "Exon" information available for 1I5F)

(-) Sequences/Alignments

Asymmetric/Biological 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:66
 aligned with CSPB_BACCL | P41016 from UniProtKB/Swiss-Prot  Length:66

    Alignment length:66
                                    10        20        30        40        50        60      
            CSPB_BACCL    1 MQRGKVKWFNNEKGYGFIEVEGGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAANVVKL 66
               SCOP domains d1i5fa_ A: Major cold shock protein                                SCOP domains
               CATH domains 1i5fA00 A:1-66 Nucleic acid-binding proteins                       CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee....eeeeee..eeeeeee.hhh............eeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------COLD_SHOCK         --------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  1i5f A  1 MQEGKVKWFNNEKGYGFIEVEGGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAANVVKL 66
                                    10        20        30        40        50        60      


Chain B from PDB  Type:PROTEIN  Length:66
 aligned with CSPB_BACCL | P41016 from UniProtKB/Swiss-Prot  Length:66

    Alignment length:66
                                    10        20        30        40        50        60      
            CSPB_BACCL    1 MQRGKVKWFNNEKGYGFIEVEGGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAANVVKL 66
               SCOP domains d1i5fb_ B: Major cold shock protein                                SCOP domains
               CATH domains 1i5fB00 B:1-66 Nucleic acid-binding proteins                       CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee....eeeee......eeee.hhh............eeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------COLD_SHOCK         --------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  1i5f B  1 MQEGKVKWFNNEKGYGFIEVEGGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAANVVKL 66
                                    10        20        30        40        50        60
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I5F)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CSPB_BACCL | P41016)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1i5f)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1i5f
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CSPB_BACCL | P41016
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  CSPB_BACCL | P41016
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CSPB_BACCL | P41016: 1c9o 1hz9 1hza 1hzb 1hzc 2hax 5jx4

(-) Related Entries Specified in the PDB File

1c9o 1C9O IS BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN
1csp 1CSP IS BACILLUS SUBTILIS COLD-SHOCK PROTEIN
1hz9 1HZ9 IS BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN E46A MUTANT
1hza 1HZA IS BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN V64T/L66E/ 67A MUTANT
1hzb 1HZB IS BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN L66E MUTANT
1hzc 1HZC IS BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN R3E/E46A/ L66E MUTANT