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

(-) Description

Title :  CRYSTAL STRUCTURE OF MONOMERIC BACTERIOPHYTOCHROME MUTANT D207L Y263F AT 1.5 A RESOLUTION USING A HOME SOURCE.
 
Authors :  S. Bhattacharya, K. A. Satyshur, H. Lehtivuori, K. T. Forest
Date :  12 May 15  (Deposition) - 20 Jan 16  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Bacteriophytochrome, Pas, Gaf, Biliverdin, Signaling Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Lehtivuori, S. Bhattacharya, N. M. Angenent-Mari, K. A. Satyshur, K. T. Forest
Removal Of Chromophore-Proximal Polar Atoms Decreases Water Content And Increases Fluorescence In A Near Infrared Phytofluor.
Front Mol Biosci V. 2 65 2015
PubMed-ID: 26636092  |  Reference-DOI: 10.3389/FMOLB.2015.00065

(-) Compounds

Molecule 1 - BACTERIOPHYTOCHROME
    Chains: A
    EC Number: 2.7.13.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: DE3
    Expression System Vector Type: PLASMID
    Gene: BPHP, DR_A0050
    Mutation: YES
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 243230
    Other Details: T7 EXPRESSION VECTOR IS ON THE N-TERMINAL END AND IS PRESENT IN THE CRYSTALLIZED PROTEIN BUT NOT SEEN.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
    Synonym: PHYTOCHROME-LIKE PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1LBV1Ligand/Ion3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC ACID
2LBW1Ligand/Ion3-[2-[(Z)-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E,4R)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC ACID
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:24 , MET A:174 , TYR A:176 , PHE A:203 , LEU A:207 , ILE A:208 , PRO A:209 , TYR A:216 , ARG A:254 , THR A:256 , SER A:257 , HIS A:260 , PHE A:263 , SER A:272 , SER A:274 , HIS A:290 , LBW A:402 , HOH A:515 , HOH A:516 , HOH A:524 , HOH A:571 , HOH A:628 , HOH A:659 , HOH A:755binding site for residue LBV A 401
2AC2SOFTWARECYS A:24 , MET A:174 , TYR A:176 , PHE A:198 , PHE A:203 , LEU A:207 , ILE A:208 , PRO A:209 , TYR A:216 , ARG A:254 , SER A:257 , MET A:259 , HIS A:260 , PHE A:263 , SER A:272 , SER A:274 , HIS A:290 , LBV A:401 , HOH A:515 , HOH A:516 , HOH A:571 , HOH A:628 , HOH A:659binding site for residue LBW A 402
3AC3SOFTWAREARG A:165 , ARG A:192 , GLU A:193 , ARG A:202 , HOH A:520 , HOH A:528 , HOH A:566binding site for residue PO4 A 403
4AC4SOFTWAREGLY A:15 , GLY A:16 , PRO A:17 , GLU A:18 , ARG A:265 , ASN A:266binding site for residue PEG A 404
5AC5SOFTWAREPHE A:178 , ALA A:179 , PRO A:180 , ALA A:182 , LEU A:283 , HOH A:672binding site for residue PEG A 405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:235 -Pro A:236

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZRR)

(-) 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:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.......hhhhh......ee....eeeeee.....eeeee.hhhhhhh.hhhhhh..hhhhhh..hhhhhhhhh.........eeeeeee...eeeeeeeeee..eeeeeeee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..........eehhhhhhhhhhhhhhhh.eeee.......eeee.....................hhhhhhhhhhh...eeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zrr A   7 PFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDWPAAGHLSLTVHRVGELLILEFEPTEHALRNAMSALESAPNLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASLIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQFLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLEYLGRELSEQVQVKEALE 323
                                    16        26        36        46        56        66        76        86        96       106       116       126   ||  143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323
                                                                                                                                                     130|                                                                                                                                                                                         
                                                                                                                                                      138
   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  (0, 0)

(no "SCOP Domain" information available for 4ZRR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    LBV  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    LBW  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:235 - Pro A:236   [ RasMol ]  
 

(-) 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
  4zrr
    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
  BPHY_DEIRA | Q9RZA4
    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)
  2.7.13.3
    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
  BPHY_DEIRA | Q9RZA4
    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
        BPHY_DEIRA | Q9RZA4: 1ztu 2o9b 2o9c 3s7n 3s7o 3s7p 3s7q 4cqh 4ijg 4o01 4o0p 4o8g 4q0h 4q0i 4q0j 4y3i 4y5f 4z1w 5ajg 5c5k 5k5b 5l8m 5lbr 5mg0 5mg1

(-) Related Entries Specified in the PDB File

3s7q