Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  STRUCTURAL GENOMICS, THE CRYSTAL STRUCTURE OF A PUTATIVE HYDROXYLASE FROM RHODOCOCCUS SP. RHA1
 
Authors :  K. Tan, T. Skarina, O. Kagen, A. Savchenko, A. Edwards, A. Joachimiak, M Center For Structural Genomics (Mcsg)
Date :  01 Feb 07  (Deposition) - 06 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (2x)
Keywords :  Apc7385, Putative Hydroxylase, Rhodococcus Sp. Rha1, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, T. Skarina, O. Kagen, A. Savchenko, A. Edwards, A. Joachimiak
The Crystal Structure Of A Putative Hydroxylase From Rhodococcus Sp. Rha1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYDROXYLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: RHA1_RO05068
    Organism Scientific: RHODOCOCCUS SP.
    Organism Taxid: 101510
    Strain: RHA1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 35)

Asymmetric Unit (2, 35)
No.NameCountTypeFull Name
1ACT12Ligand/IonACETATE ION
2MSE23Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 17)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2MSE11Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 18)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 70)
No.NameCountTypeFull Name
1ACT24Ligand/IonACETATE ION
2MSE46Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:205 , ARG A:213 , HOH A:821BINDING SITE FOR RESIDUE ACT A 601
02AC2SOFTWAREPRO B:159 , ASN B:205 , ARG B:213BINDING SITE FOR RESIDUE ACT B 602
03AC3SOFTWAREARG B:313 , ARG B:388BINDING SITE FOR RESIDUE ACT B 603
04AC4SOFTWAREARG A:259 , HOH A:865 , HOH A:886BINDING SITE FOR RESIDUE ACT A 604
05AC5SOFTWAREGLY A:129 , ASN B:104 , ASP B:105BINDING SITE FOR RESIDUE ACT B 605
06AC6SOFTWAREARG B:37 , ASP B:105 , TRP B:107 , HIS B:139 , HOH B:762BINDING SITE FOR RESIDUE ACT B 606
07AC7SOFTWAREASP A:211 , PHE A:310 , ARG A:313 , ARG A:388BINDING SITE FOR RESIDUE ACT A 607
08AC8SOFTWAREGLU A:279 , HOH A:670 , ARG B:329 , PRO B:367BINDING SITE FOR RESIDUE ACT B 608
09AC9SOFTWAREGLY B:2 , VAL B:4 , GLU B:59 , HOH B:878BINDING SITE FOR RESIDUE ACT B 609
10BC1SOFTWAREVAL A:366 , PRO A:367 , GLY A:368 , PRO A:369 , HOH A:883 , TYR B:272 , VAL B:273 , ARG B:337 , HOH B:883BINDING SITE FOR RESIDUE ACT A 610
11BC2SOFTWARETRP A:325 , ARG A:329 , ASP A:332 , HIS A:357 , LEU A:360 , GLU B:333 , ALA B:336BINDING SITE FOR RESIDUE ACT A 611
12BC3SOFTWAREARG A:213BINDING SITE FOR RESIDUE ACT A 612

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OR0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:110 -Pro A:111
2Ser B:110 -Pro B:111

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OR0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OR0)

(-) Exons   (0, 0)

(no "Exon" information available for 2OR0)

(-) 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:385
 aligned with Q0S6I7_RHOJR | Q0S6I7 from UniProtKB/TrEMBL  Length:391

    Alignment length:390
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391
         Q0S6I7_RHOJR     2 GRVLDRIEVVAEEIRGQAVQSEADCRLTDAAAGLLRDSGAIRLLQPRLYGGYEVHPREFAETVMGVAALDGASGWVTGIVGVHPWELAFADPQVQEEIWGEDNDTWMASPYAPMGVATPVDGGYVLKGRWSFSSGTDHCQWAFLGAMVGDGEGGIATPSSLHVILPRTDYQIVEDTWDVIGLRGTGSKDLIVDGAFVPGYRTLNAAKVMDGRAQKEAGRPEPLFNMPYSCMFPLGITAAVIGITEGALACHIAVQKDRVAITGQKIKEDPYVLSAIGESAAEINASRVSLIETADRFYDKVDAGKEITFEERAIGRRTQIAAAWRAVRAADEIFARAGGGALHYKTPMQRFWRDAHAGLAHAVHVPGPTNHASALTQLGGEPQGMMRAMI 391
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2or0A01 A:2-106 Butyryl-Coa Dehydrogenase, subunit A, domain 1                                           2or0A02 A:107-205 Butyryl-CoA Dehydrogenase,      subunit A, domain 2                              2or0A03 A:206-391 Butyryl-CoA Dehydrogenase, subunit A, domain 3                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......ee......eeeeee..eeeeeeeeeee.hhhhh.eeeeeeee..-----....eeeeeee.hhheee........hhhhh.eeeeeeeeeee...eeehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2or0 A   2 GRVLDRIEVVAEEIRGQAVQSEADCRLTDAAAGLLRDSGAIRLLQPRLYGGYEVHPREFAETVmGVAALDGASGWVTGIVGVHPWELAFADPQVQEEIWGEDNDTWmASPYAPmGVATPVDGGYVLKGRWSFSSGTDHCQWAFLGAmVGD-----ATPSSLHVILPRTDYQIVEDTWDVIGLRGTGSKDLIVDGAFVPGYRTLNAAKVmDGRAQKEAGRPEPLFNmPYSCmFPLGITAAVIGITEGALACHIAVQKDRVAITGQKIKEDPYVLSAIGESAAEINASRVSLIETADRFYDKVDAGKEITFEERAIGRRTQIAAAWRAVRAADEIFARAGGGALHYKTPmQRFWRDAHAGLAHAVHVPGPTNHASALTQLGGEPQGmmRAmI 391
                                    11        21        31        41        51        61   |    71        81        91       101      |111   |   121       131       141      |151     | 161       171       181       191       201       211       221     | 231|      241       251       261       271       281       291       301       311       321       331       341       351       361       371       381    || 391
                                                                                          65-MSE                                    108-MSE  |                              148-MSE  157                                                  210-MSE          227-MSE|                                                                                                                  349-MSE                              386-MSE 
                                                                                                                                           115-MSE                             151                                                                              232-MSE                                                                                                                                                    387-MSE
                                                                                                                                                                                                                                                                                                                                                                                                                              390-MSE


Chain B from PDB  Type:PROTEIN  Length:409
 aligned with Q0S6I7_RHOJR | Q0S6I7 from UniProtKB/TrEMBL  Length:391

    Alignment length:409
                                              1                                                                                                                                                                                                                                                                                                                                                                                                      
                                     -        |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382         
         Q0S6I7_RHOJR     - ------------------MGRVLDRIEVVAEEIRGQAVQSEADCRLTDAAAGLLRDSGAIRLLQPRLYGGYEVHPREFAETVMGVAALDGASGWVTGIVGVHPWELAFADPQVQEEIWGEDNDTWMASPYAPMGVATPVDGGYVLKGRWSFSSGTDHCQWAFLGAMVGDGEGGIATPSSLHVILPRTDYQIVEDTWDVIGLRGTGSKDLIVDGAFVPGYRTLNAAKVMDGRAQKEAGRPEPLFNMPYSCMFPLGITAAVIGITEGALACHIAVQKDRVAITGQKIKEDPYVLSAIGESAAEINASRVSLIETADRFYDKVDAGKEITFEERAIGRRTQIAAAWRAVRAADEIFARAGGGALHYKTPMQRFWRDAHAGLAHAVHVPGPTNHASALTQLGGEPQGMMRAMI 391
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2or0B01 B:-17-106 Butyryl-Coa Dehydrogenase, subunit A, domain 1                                                            2or0B02 B:107-205 Butyryl-CoA Dehydrogenase, subunit A, domain 2                                   2or0B03 B:206-391 Butyryl-CoA Dehydrogenase, subunit A, domain 3                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.....ee.hhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......ee......eeeeee..eeeeeeeeeee.hhhhh.eeeeeeee...........eeeeeee.hhheee........hhhhh.eeeeeeeeeee...eeehhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2or0 B -17 SHHHHHHSSGRENLYFQGmGRVLDRIEVVAEEIRGQAVQSEADCRLTDAAAGLLRDSGAIRLLQPRLYGGYEVHPREFAETVmGVAALDGASGWVTGIVGVHPWELAFADPQVQEEIWGEDNDTWmASPYAPmGVATPVDGGYVLKGRWSFSSGTDHCQWAFLGAmVGDGEGGIATPSSLHVILPRTDYQIVEDTWDVIGLRGTGSKDLIVDGAFVPGYRTLNAAKVmDGRAQKEAGRPEPLFNmPYSCmFPLGITAAVIGITEGALACHIAVQKDRVAITGQKIKEDPYVLSAIGESAAEINASRVSLIETADRFYDKVDAGKEITFEERAIGRRTQIAAAWRAVRAADEIFARAGGGALHYKTPmQRFWRDAHAGLAHAVHVPGPTNHASALTQLGGEPQGmmRAmI 391
                                    -8        |2        12        22        32        42        52        62  |     72        82        92       102     | 112  |    122       132       142     | 152       162       172       182       192       202       212       222    |  232       242       252       262       272       282       292       302       312       322       332       342      |352       362       372       382   ||  | 
                                              1-MSE                                                          65-MSE                                    108-MSE  |                              148-MSE                                                       210-MSE          227-MSE|                                                                                                                  349-MSE                              386-MSE 
                                                                                                                                                              115-MSE                                                                                                              232-MSE                                                                                                                                                    387-MSE
                                                                                                                                                                                                                                                                                                                                                                                                                                                 390-MSE
   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 2OR0)

(-) CATH Domains  (3, 6)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2OR0)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q0S6I7_RHOJR | Q0S6I7)
molecular function
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0016627    oxidoreductase activity, acting on the CH-CH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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.

 Visualization

(-) Interactive Views

Asymmetric 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:110 - Pro A:111   [ RasMol ]  
    Ser B:110 - Pro B:111   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 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
  2or0
    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
  Q0S6I7_RHOJR | Q0S6I7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q0S6I7_RHOJR | Q0S6I7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2OR0)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2OR0)