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(-) Description

Title :  A DOMAIN OF A FUNCTIONALLY UNKNOWN PROTEIN FROM METHANOCALDOCOCCUS JANNASCHII DSM 2661.
 
Authors :  K. Tan, G. Chhor, G. Cobb, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  09 Jul 09  (Deposition) - 21 Jul 09  (Release) - 21 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.64
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Apc89320. 5, Methanocaldococcus Jannaschii Dsm 2661, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Rna-Binding, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, G. Chhor, G. Cobb, A. Joachimiak
A Domain Of A Functionally Unknown Protein From Methanocaldococcus Jannaschii Dsm 2661.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KH DOMAIN-CONTAINING PROTEIN MJ1533
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: PPK1037
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 27-165
    Gene: METHANOCALDOCOCCUS JANNASCHII
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Strain: DSM 2661

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric Unit (5, 9)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3FMT3Ligand/IonFORMIC ACID
4MSE2Mod. Amino AcidSELENOMETHIONINE
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3FMT3Ligand/IonFORMIC ACID
4MSE2Mod. Amino AcidSELENOMETHIONINE
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (4, 16)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3FMT6Ligand/IonFORMIC ACID
4MSE4Mod. Amino AcidSELENOMETHIONINE
5PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:137BINDING SITE FOR RESIDUE CL A 1
2AC2SOFTWAREGLU A:154BINDING SITE FOR RESIDUE PEG A 166
3AC3SOFTWAREASN A:94 , LYS A:96 , GLU A:102BINDING SITE FOR RESIDUE FMT A 167
4AC4SOFTWARELYS A:28 , ASN A:129 , GLU A:149BINDING SITE FOR RESIDUE FMT A 2
5AC5SOFTWAREVAL A:163 , ASP A:165BINDING SITE FOR RESIDUE FMT A 3
6AC6SOFTWAREARG A:40 , ASP A:165BINDING SITE FOR RESIDUE ACT A 168
7AC7SOFTWAREARG A:40 , GLU A:154 , GLU A:161 , LEU A:162BINDING SITE FOR RESIDUE ACT A 169

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I8O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3I8O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I8O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3I8O)

(-) Exons   (0, 0)

(no "Exon" information available for 3I8O)

(-) 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:140
 aligned with Y1533_METJA | Q58928 from UniProtKB/Swiss-Prot  Length:642

    Alignment length:140
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165
          Y1533_METJA    26 GKKVCVDTCVVIDGRITELIERGKLKDATIIIPEAVVSELEYQANMGREIGYKGIEELRKLIEKASEHNIKVEYYGERPTREEIFLAKSGEIDAMIRKVAKETNSILLTSDWIQYNLAKAQGIEAYFLEAAEEEVELVLD 165
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhh....hhhhhhhhhhhhh..eeee.hhhhhhhhhhh...eee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i8o A  26 AKKVCVDTCVVIDGRITELIERGKLKDATIIIPEAVVSELEYQANmGREIGYKGIEELRKLIEKASEHNIKVEYYGERPTREEIFLAKSGEIDAmIRKVAKETNSILLTSDWIQYNLAKAQGIEAYFLEAAEEEVELVLD 165
                                    35        45        55        65     |  75        85        95       105       115    |  125       135       145       155       165
                                                                        71-MSE                                          120-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3I8O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3I8O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I8O)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Y1533_METJA | Q58928)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

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