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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE DNA BINDING PROTEIN (APE_0880A) FROM AEROPYRUM PERNIX K1 AT 2.21 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  06 Apr 07  (Deposition) - 24 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Biol. Unit 3:  A,B  (2x)
Biol. Unit 4:  A,B  (2x)
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Uncharacterized Protein (Np_147569. 1) From Aeropyrum Pernix At 2. 21 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED 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: NP_147569.1, APE0880.1, APES039, APE_0880A
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 272557
    Strain: K1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB
Biological Unit 3 (2x): AB
Biological Unit 4 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric Unit (5, 15)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2CL3Ligand/IonCHLORIDE ION
3EDO7Ligand/Ion1,2-ETHANEDIOL
4MSE3Mod. Amino AcidSELENOMETHIONINE
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (4, 12)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2CL-1Ligand/IonCHLORIDE ION
3EDO7Ligand/Ion1,2-ETHANEDIOL
4MSE3Mod. Amino AcidSELENOMETHIONINE
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (4, 24)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2CL-1Ligand/IonCHLORIDE ION
3EDO14Ligand/Ion1,2-ETHANEDIOL
4MSE6Mod. Amino AcidSELENOMETHIONINE
5PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 3 (4, 24)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2CL-1Ligand/IonCHLORIDE ION
3EDO14Ligand/Ion1,2-ETHANEDIOL
4MSE6Mod. Amino AcidSELENOMETHIONINE
5PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 4 (4, 24)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2CL-1Ligand/IonCHLORIDE ION
3EDO14Ligand/Ion1,2-ETHANEDIOL
4MSE6Mod. Amino AcidSELENOMETHIONINE
5PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN B:9 , HIS B:12 , ARG B:53BINDING SITE FOR RESIDUE CL B 95
02AC2SOFTWAREGLN A:9 , HIS A:12 , ARG A:53BINDING SITE FOR RESIDUE CL A 95
03AC3SOFTWARELEU B:72 , HOH B:118 , HOH B:119BINDING SITE FOR RESIDUE CL B 96
04AC4SOFTWAREMSE A:1 , ASP A:2 , GLN B:9 , GLY B:11 , HIS B:12 , ARG B:15 , VAL B:41 , SER B:42 , THR B:45BINDING SITE FOR RESIDUE CIT B 97
05AC5SOFTWARESER A:31 , LEU A:32 , ALA A:33 , GLU A:43 , ARG A:68 , VAL A:69 , LYS A:70 , EDO A:99BINDING SITE FOR RESIDUE EDO A 96
06AC6SOFTWARESER A:31 , GLU A:34 , TYR B:67BINDING SITE FOR RESIDUE EDO A 97
07AC7SOFTWAREHIS A:12 , ARG A:15 , VAL A:41 , SER A:42 , THR A:45 , HOH A:105BINDING SITE FOR RESIDUE EDO A 98
08AC8SOFTWARELEU A:32 , LYS A:51 , GLU A:62 , EDO A:96 , HOH A:108BINDING SITE FOR RESIDUE EDO A 99
09AC9SOFTWAREPHE B:46 , PHE B:47 , MSE B:48 , GLY B:49 , LEU B:50 , LYS B:51 , ASP B:52 , HOH B:108BINDING SITE FOR RESIDUE EDO B 98
10BC1SOFTWARETHR A:19 , GLU A:22 , PHE A:23 , LYS A:26BINDING SITE FOR RESIDUE EDO A 100
11BC2SOFTWARETHR B:45 , MSE B:48 , ARG B:53BINDING SITE FOR RESIDUE EDO B 99
12BC3SOFTWARELEU B:32 , ALA B:33 , VAL B:36 , GLU B:43 , PHE B:47 , VAL B:69 , LYS B:70 , HOH B:111 , HOH B:113BINDING SITE FOR RESIDUE PEG B 100

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PG4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PG4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PG4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PG4)

(-) Exons   (0, 0)

(no "Exon" information available for 2PG4)

(-) 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:92
 aligned with Q9YDN4_AERPE | Q9YDN4 from UniProtKB/TrEMBL  Length:94

    Alignment length:92
                                    10        20        30        40        50        60        70        80        90  
          Q9YDN4_AERPE    1 MDDETLRLQFGHLIRILPTLLEFEKKGYEPSLAEIVKASGVSEKTFFMGLKDRLIRAGLVKEETLSYRVKTLKLTEKGRRLAECLEKCRDVL 92
               SCOP domains d2pg4a1 A:1-92 Uncharacterized protein APE0880.1                                             SCOP domains
               CATH domains -2pg4A00 A:2-92 'winged helix' repressor DNA binding domain                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhh..eeeeeee..eeeeeehhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  2pg4 A  1 mDDETLRLQFGHLIRILPTLLEFEKKGYEPSLAEIVKASGVSEKTFFmGLKDRLIRAGLVKEETLSYRVKTLKLTEKGRRLAECLEKCRDVL 92
                            |       10        20        30        40       |50        60        70        80        90  
                            |                                             48-MSE                                        
                            1-MSE                                                                                       


Chain B from PDB  Type:PROTEIN  Length:91
 aligned with Q9YDN4_AERPE | Q9YDN4 from UniProtKB/TrEMBL  Length:94

    Alignment length:91
                                    12        22        32        42        52        62        72        82        92 
          Q9YDN4_AERPE    3 DETLRLQFGHLIRILPTLLEFEKKGYEPSLAEIVKASGVSEKTFFMGLKDRLIRAGLVKEETLSYRVKTLKLTEKGRRLAECLEKCRDVLG 93
               SCOP domains d2pg4b_ B: Uncharacterized protein APE0880.1                                                SCOP domains
               CATH domains 2pg4B00 B:3-93 'winged helix' repressor DNA binding domain                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhh..eeeee.....eeeeehhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  2pg4 B  3 DETLRLQFGHLIRILPTLLEFEKKGYEPSLAEIVKASGVSEKTFFmGLKDRLIRAGLVKEETLSYRVKTLKLTEKGRRLAECLEKCRDVLG 93
                                    12        22        32        42     |  52        62        72        82        92 
                                                                        48-MSE
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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  (1, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2PG4)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2PG4)

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