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(-) Description

Title :  CRYSTAL STRUCTURE OF PROTEIN VC1899 FROM VIBRIO CHOLERAE
 
Authors :  C. Chang, A. Joachimiak, R. Wu, Midwest Center For Structural Geno (Mcsg)
Date :  04 Oct 04  (Deposition) - 16 Nov 04  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Alpha-Beta, Mcsg, Protein Structure Initiative, Structural Genomics, Psi, Midwest Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, A. Joachimiak, R. Wu, S. Moy, Midwest Center For Structural Genomics (Mcsg)
Crystal Structure Of Protein Vc1899 From Vibrio Cholerae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN VC1899
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666

 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  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1FMT6Ligand/IonFORMIC ACID
2GOL2Ligand/IonGLYCEROL
3MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1FMT6Ligand/IonFORMIC ACID
2GOL2Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 16)
No.NameCountTypeFull Name
1FMT12Ligand/IonFORMIC ACID
2GOL4Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:14 , ARG A:96 , HOH A:428BINDING SITE FOR RESIDUE MG A 409
2AC2SOFTWAREHIS A:4 , THR A:24 , VAL A:25 , SER A:26 , LYS A:88 , GOL A:402 , HOH A:542 , HOH A:689BINDING SITE FOR RESIDUE GOL A 401
3AC3SOFTWAREGOL A:401 , HOH A:484 , HOH A:572 , HOH A:686 , HOH A:709 , HOH A:779BINDING SITE FOR RESIDUE GOL A 402
4AC4SOFTWAREASN A:131 , ASN A:132 , ASP A:133 , HOH A:537 , HOH A:552 , HOH A:759BINDING SITE FOR RESIDUE FMT A 403
5AC5SOFTWAREARG A:51 , ASN A:52 , PRO A:61 , ASN A:65 , ALA A:68 , HOH A:453 , HOH A:477 , HOH A:673BINDING SITE FOR RESIDUE FMT A 404
6AC6SOFTWARELYS A:70 , ARG A:74 , HOH A:548BINDING SITE FOR RESIDUE FMT A 405
7AC7SOFTWAREASP A:165 , LEU A:168 , TYR A:169 , THR A:254 , SER A:258 , HOH A:467BINDING SITE FOR RESIDUE FMT A 406
8AC8SOFTWARETYR A:213 , GLU A:215 , LEU A:216 , HOH A:726BINDING SITE FOR RESIDUE FMT A 407
9AC9SOFTWARETYR A:321 , ARG A:352 , ASP A:355 , HOH A:635BINDING SITE FOR RESIDUE FMT A 408

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:127 -Pro A:128

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XMX)

(-) Exons   (0, 0)

(no "Exon" information available for 1XMX)

(-) 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:380
 aligned with Q9KQU9_VIBCH | Q9KQU9 from UniProtKB/TrEMBL  Length:383

    Alignment length:385
                              1                                                                                                                                                                                                                                                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378     
         Q9KQU9_VIBCH     - --MAIHVGIIDQDPVRLVTPLLDHRTVSRHIIFIGDHTQTVIYQRLSDVLNKRNISTDFFEIPAGSNTSAIKSAIRELAETLKARGEEVKFNASCGLRHRLLSAYEVFRSYHWPIFVVEPNSDCLCWLYPEGNNDTQVQDRITIADYLTIFGARGEFNEHQLSPQLDQQLYQLGERWASNALELGPGLATLNYLATTCRKEQKLDVELSDKQQGYRELNLLLSDLVEAKIASYENGILTFINEEARRFANGEWLETLVHSTVKQIQDDMPTIQDRSLNVQVYRQLGEREVRNELDVATVVNNKLHIIECKTKGMRDDGDDTLYKLESLRDLLGGLQARAMLVSFRPLRHNDITRAEDLGLALIGPDELKDLKTHLTQWFKAAGGN 383
               SCOP domains d1xmxa_ A: Hypothetical protein VC1899                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------1xmxA02              -----------------------------------------------------------------------------------------1xmxA02 A:141-161,A:251-383  [code=3.40.1350.10, no name define d]                                                                    CATH domains
               Pfam domains --DUF1887-1xmxA01 A:1-380                                                                                                                                                                                                                                                                                                                                                                     --- Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhh......eeeeeehhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh...eeee.....eeeeee......ee.....hhhhhhhhh..eee..----hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhh..eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeeeeee..eeeeeeeeeeeee..eeeeeeee.....-...hhhhhhhhhhhhhhhhhheeeeee....hhhhhhhhhhhh.eeehhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xmx A  -1 NAMAIHVGIIDQDPVRLVTPLLDHRTVSRHIIFIGDHTQTVIYQRLSDVLNKRNISTDFFEIPAGSNTSAIKSAIRELAETLKARGEEVKFNASCGLRHRLLSAYEVFRSYHWPIFVVEPNSDCLCWLYPEGNNDTQVQDRITIADYLTIFGARGEFN----SPQLDQQLYQLGERWASNALELGPGLATLNYLATTCRKEQKLDVELSDKQQGYRELNLLLSDLVEAKIASYENGILTFINEEARRFANGEWLETLVHSTVKQIQDDMPTIQDRSLNVQVYRQLGEREVRNELDVATVVNNKLHIIECKTKGMR-DGDDTLYKLESLRDLLGGLQARAMLVSFRPLRHNDITRAEDLGLALIGPDELKDLKTHLTQWFKAAGGN 383
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       | -  |    168       178       188       198       208       218       228       238       248       258       268       278       288       298       308    | |318       328       338       348       358       368       378     
                                                                                                                                                                                       156  161                                                                                                                                                     313 |                                                                    
                                                                                                                                                                                                                                                                                                                                                      315
   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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: PDDEXK (13)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9KQU9_VIBCH | Q9KQU9)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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