Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (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 :  24 Jan 01  (Deposition) - 07 Nov 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1HZA)

(-) Sites  (0, 0)

(no "Site" information available for 1HZA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 1HZA)

(-) 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:67
 aligned with CSPB_BACCL | P41016 from UniProtKB/Swiss-Prot  Length:66

    Alignment length:67
                                                                                            66 
                                    10        20        30        40        50        60     | 
            CSPB_BACCL    1 MQRGKVKWFNNEKGYGFIEVEGGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAANVVKL-  -
               SCOP domains d1hzaa_ A: Major cold shock protein                                 SCOP domains
               CATH domains 1hzaA00 A:1-67 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
                  1hza A  1 MQRGKVKWFNNEKGYGFIEVEGGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAANVTKEA 67
                                    10        20        30        40        50        60       


Chain B from PDB  Type:PROTEIN  Length:67
 aligned with CSPB_BACCL | P41016 from UniProtKB/Swiss-Prot  Length:66

    Alignment length:67
                                                                                            66 
                                    10        20        30        40        50        60     | 
            CSPB_BACCL    1 MQRGKVKWFNNEKGYGFIEVEGGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAANVVKL-  -
               SCOP domains d1hzab_ B: Major cold shock protein                                 SCOP domains
               CATH domains 1hzaB00 B:1-67 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
                  1hza B  1 MQRGKVKWFNNEKGYGFIEVEGGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAANVTKEA 67
                                    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 1HZA)

(-) 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
(no "Ligands, Modified Residues, Ions" information available for 1hza)
 
  Sites
(no "Sites" information available for 1hza)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1hza)
 

(-) 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 ](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
  1hza
    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 1hzb 1hzc 1i5f 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 SINGLE MUTANT OF 1C9O (E46A)
1hzb 1HZB IS SINGLE MUTANT OF 1C9O (L66E)
1hzc 1HZC IS TRIPLE MUTANT OF 1C9O (R3E/E46A/L66E)