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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE 2OG-FE(II) OXYGENASE FAMILY PROTEIN (CC_0200) FROM CAULOBACTER CRESCENTUS AT 1.44 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  31 Aug 10  (Deposition) - 01 Dec 10  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.44
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Putative 2Og-Fe(Ii) Oxygenase Family Protein (Cc_0200) From Caulobacter Crescentus At 1. 44 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE 2OG-FE(II) OXYGENASE FAMILY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CC_0200
    Organism Common: CAULOBACTER VIBRIOIDES
    Organism Scientific: CAULOBACTER CRESCENTUS CB15
    Organism Taxid: 190650
    Synonym: OXIDOREDUCTASE IRON/ASCORBATE FAMILY

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 29)

Asymmetric Unit (3, 29)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO20Ligand/Ion1,2-ETHANEDIOL
3MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO10Ligand/Ion1,2-ETHANEDIOL
3MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 14)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO10Ligand/Ion1,2-ETHANEDIOL
3MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:190 , HIS A:247 , HOH A:561 , HOH A:712 , HOH A:719BINDING SITE FOR RESIDUE EDO A 314
02AC2SOFTWARELYS A:72 , ALA A:112 , HIS A:113 , ALA A:115 , HOH A:829 , GLN B:67 , HOH B:826BINDING SITE FOR RESIDUE EDO A 318
03AC3SOFTWAREPHE A:11 , TYR A:14 , ASP A:41 , LYS A:143 , HOH A:828 , ARG B:156BINDING SITE FOR RESIDUE EDO A 320
04AC4SOFTWAREGLN A:44 , GLU A:203 , PRO A:223 , GLY A:224 , HOH A:379 , HOH A:535 , HOH A:666BINDING SITE FOR RESIDUE EDO A 321
05AC5SOFTWAREARG A:236 , GLU A:293 , GLN A:303 , HOH A:731 , HOH A:785BINDING SITE FOR RESIDUE EDO A 322
06AC6SOFTWARELEU A:279 , GLN A:280 , ASN A:281BINDING SITE FOR RESIDUE EDO A 323
07AC7SOFTWAREHIS A:91 , GLU B:30 , ARG B:31 , HOH B:857 , HOH B:1078BINDING SITE FOR RESIDUE EDO A 324
08AC8SOFTWAREGLU A:155 , ASP A:157 , PHE A:158 , PRO A:161 , HOH A:343 , HOH A:948BINDING SITE FOR RESIDUE EDO A 326
09AC9SOFTWAREALA A:115 , ASP A:116 , VAL B:71 , LYS B:72 , HOH B:1091BINDING SITE FOR RESIDUE EDO A 328
10BC1SOFTWARETRP A:119 , PRO A:120 , ILE A:123 , PRO A:124 , PHE A:126 , LYS A:127 , HOH A:363BINDING SITE FOR RESIDUE EDO A 330
11BC2SOFTWAREARG A:109 , ARG B:109BINDING SITE FOR RESIDUE CL A 332
12BC3SOFTWARELYS B:72 , ARG B:111 , ALA B:112 , EDO B:329 , HOH B:675 , HOH B:728 , HOH B:802BINDING SITE FOR RESIDUE EDO B 312
13BC4SOFTWAREARG A:156 , PHE B:11 , TYR B:14 , ASP B:41 , LYS B:143 , EDO B:331 , HOH B:840BINDING SITE FOR RESIDUE EDO B 313
14BC5SOFTWAREHIS B:190 , HIS B:247 , HOH B:604 , HOH B:724 , HOH B:742BINDING SITE FOR RESIDUE EDO B 315
15BC6SOFTWAREALA B:59 , LEU B:60 , PRO B:61 , ASP B:289 , HOH B:725 , HOH B:819 , HOH B:931 , HOH B:1173BINDING SITE FOR RESIDUE EDO B 316
16BC7SOFTWARELEU B:152 , LYS B:153 , ASN B:281 , HOH B:919 , HOH B:1166BINDING SITE FOR RESIDUE EDO B 317
17BC8SOFTWAREPHE B:11 , SER B:12 , TYR B:14 , ALA B:15 , HOH B:595 , HOH B:937BINDING SITE FOR RESIDUE EDO B 319
18BC9SOFTWAREPRO B:120 , ILE B:123 , PRO B:124 , PHE B:126 , LYS B:127BINDING SITE FOR RESIDUE EDO B 325
19CC1SOFTWAREGLU B:155 , ASP B:157 , PHE B:158 , PRO B:161 , HOH B:341 , HOH B:838BINDING SITE FOR RESIDUE EDO B 327
20CC2SOFTWAREGLN A:67 , HOH A:824 , LYS B:72 , ALA B:112 , HIS B:113 , EDO B:312 , HOH B:854BINDING SITE FOR RESIDUE EDO B 329
21CC3SOFTWAREASP B:41 , LEU B:42 , SER B:136 , GLY B:139 , MSE B:140 , LYS B:143 , EDO B:313BINDING SITE FOR RESIDUE EDO B 331

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OOX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OOX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OOX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OOX)

(-) Exons   (0, 0)

(no "Exon" information available for 3OOX)

(-) 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:305
 aligned with Q9ABM7_CAUCR | Q9ABM7 from UniProtKB/TrEMBL  Length:311

    Alignment length:307
                                    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       
         Q9ABM7_CAUCR     3 TSAIDPVSFSLYAKDFTRFAQELGASFERYGFAVLSDYDLDQARIDAAVDSAKAFFALPVETKKQYAGVKGGARGYIPFGVETAKGADHYDLKEFWHMGRDLPPGHRFRAHMADNVWPAEIPAFKHDVSWLYNSLDGMGGKVLEAIATYLKLERDFFKPTVQDGNSVLRLLHYPPIPKDATGVRAGAHGDINTITLLLGAEEGGLEVLDRDGQWLPINPPPGCLVINIGDMLERLTNNVLPSTVHRVVNPPPERRGVPRYSTPFFLHFASDYEIKTLQNCVTAENPDRYPESITADEFLQQRLREIK 309
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eehhhhhhhhhhhhhhhhhhhhhhheeeee....hhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhh.eee................eeeee.......hhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh....eeeeeee........--.eeee.....eeeee......eeee.....eee.......eeeeehhhhhhhh........eee...hhhhh...eee..eee......ee..hhhhh...........eehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oox A   3 TSAIDPVSFSLYAKDFTRFAQELGASFERYGFAVLSDYDLDQARIDAAVDSAKAFFALPVETKKQYAGVKGGARGYIPFGVETAKGADHYDLKEFWHmGRDLPPGHRFRAHmADNVWPAEIPAFKHDVSWLYNSLDGmGGKVLEAIATYLKLERDFFKPTVQDGNSVLRLLHYPPIPKDAT--RAGAHGDINTITLLLGAEEGGLEVLDRDGQWLPINPPPGCLVINIGDmLERLTNNVLPSTVHRVVNPPPERRGVPRYSTPFFLHFASDYEIKTLQNCVTAENPDRYPESITADEFLQQRLREIK 309
                                    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       
                                                                                                                           100-MSE       114-MSE                   140-MSE                                    183  |                                            233-MSE                                                                        
                                                                                                                                                                                                                 186                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:305
 aligned with Q9ABM7_CAUCR | Q9ABM7 from UniProtKB/TrEMBL  Length:311

    Alignment length:306
                                    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      
         Q9ABM7_CAUCR     3 TSAIDPVSFSLYAKDFTRFAQELGASFERYGFAVLSDYDLDQARIDAAVDSAKAFFALPVETKKQYAGVKGGARGYIPFGVETAKGADHYDLKEFWHMGRDLPPGHRFRAHMADNVWPAEIPAFKHDVSWLYNSLDGMGGKVLEAIATYLKLERDFFKPTVQDGNSVLRLLHYPPIPKDATGVRAGAHGDINTITLLLGAEEGGLEVLDRDGQWLPINPPPGCLVINIGDMLERLTNNVLPSTVHRVVNPPPERRGVPRYSTPFFLHFASDYEIKTLQNCVTAENPDRYPESITADEFLQQRLREI 308
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---DIOX_N-3ooxB03 B:6-122                                                                                               -------------------------------------------2OG-FeII_Oxy-3ooxB 01 B:166-270                                                                          -------------------------------------- Pfam domains (1)
           Pfam domains (2) ---DIOX_N-3ooxB04 B:6-122                                                                                               -------------------------------------------2OG-FeII_Oxy-3ooxB 02 B:166-270                                                                          -------------------------------------- Pfam domains (2)
         Sec.struct. author ......eehhhhhhhhhhhhhhhhhhhhhhheeeee....hhhhhhhhhhhhhhhhh.hhhhhhh.........eee................eeeee.......hhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh....eeeeeee........-..eeee.....eeeee......eeee.....eee.......eeeeehhhhhhhh........eee...hhhhh...eee..eee......ee..hhhhh...........eehhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oox B   3 TSAIDPVSFSLYAKDFTRFAQELGASFERYGFAVLSDYDLDQARIDAAVDSAKAFFALPVETKKQYAGVKGGARGYIPFGVETAKGADHYDLKEFWHmGRDLPPGHRFRAHmADNVWPAEIPAFKHDVSWLYNSLDGmGGKVLEAIATYLKLERDFFKPTVQDGNSVLRLLHYPPIPKDAT-VRAGAHGDINTITLLLGAEEGGLEVLDRDGQWLPINPPPGCLVINIGDmLERLTNNVLPSTVHRVVNPPPERRGVPRYSTPFFLHFASDYEIKTLQNCVTAENPDRYPESITADEFLQQRLREI 308
                                    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      
                                                                                                                           100-MSE       114-MSE                   140-MSE                                    183 |                                             233-MSE                                                                       
                                                                                                                                                                                                                185
   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 3OOX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OOX)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: Cupin (179)
(-)
Clan: no clan defined [family: DIOX_N] (24)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9ABM7_CAUCR | Q9ABM7)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ 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 ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3oox)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  3oox
    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
  Q9ABM7_CAUCR | Q9ABM7
    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
  Q9ABM7_CAUCR | Q9ABM7
    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 3OOX)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3OOX)