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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE DNA BINDING PROTEIN NE0471 FROM NITROSOMONAS EUROPAEA ATCC 19718
 
Authors :  Y. Kim, A. Joachimiak, T. Skarina, A. Savchenko, A. Edwards, Midwest C Structural Genomics (Mcsg)
Date :  29 Aug 05  (Deposition) - 11 Oct 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  B  (2x)
Keywords :  Alpha-Beta Structure, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, A. Joachimiak, T. Skarina, A. Savchenko, A. Edwards
Crystal Structure Of The Hypothetical Protein Ne0471 From Nitrosomonas Europaea
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN NE0471
    Atcc: 19718
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: NITROSOMONAS EUROPAEA
    Organism Taxid: 915

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2GOL2Ligand/IonGLYCEROL
3MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2GOL2Ligand/IonGLYCEROL
3MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1FMT-1Ligand/IonFORMIC ACID
2GOL2Ligand/IonGLYCEROL
3MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (3, 12)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2GOL2Ligand/IonGLYCEROL
3MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:48 , TYR B:4 , SER B:119 , TYR B:120 , THR B:123 , HIS B:125 , HOH B:1240 , HOH B:1311BINDING SITE FOR RESIDUE GOL B 1201
2AC2SOFTWAREASP A:33 , VAL A:34 , ASP A:36 , ILE A:37 , TRP A:80 , HOH A:1221 , HOH A:1239BINDING SITE FOR RESIDUE GOL A 1202
3AC3SOFTWAREARG B:39 , GLU B:91 , ASP B:95 , HOH B:1360 , HOH B:1374BINDING SITE FOR RESIDUE FMT B 1205

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Pro A:17 -Tyr A:18
2Arg A:143 -Pro A:144
3Pro B:17 -Tyr B:18

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2AUW)

(-) 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:151
 aligned with Q82X29_NITEU | Q82X29 from UniProtKB/TrEMBL  Length:166

    Alignment length:151
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153 
         Q82X29_NITEU     4 YFFPKLTAVEALAPYRLRTTWSTGEVLEVDVGDILRKIPDLAPILDPEAFARVHIAEWEGSVEWFDTEFGRDNVYAWAKEQAGEVSHEMFGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKIIPRTIWLACLGWEATRPETKTLPRTLP 154
               SCOP domains d2auwa2 A:4-87 Hypothetical protein NE0471 N-terminal domain                        d2auwa1 A:88-154 Hypothetical protein NE0471 C-terminal domain      SCOP domains
               CATH domains 2auwA01 A:4-85 NE0471 N-terminal domain-like                                      2auwA02 A:86-154 lambda repressor-like DNA-binding domains            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee....eeeeee....eeeeehhhhhhhhhhhhhhhhhhhhh..ee......ee......hhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2auw A   4 YFFPKLTAVEALAPYRLRTTWSTGEVLEVDVGDILRKIPDLAPILDPEAFARVHIAEWEGSVEWFDTEFGRDNVYAWAKEQAGEVSHEmFGDWmHRNNLSLTTAAEALGISRRmVSYYRTAHKIIPRTIWLACLGWEATRPETKTLPRTLP 154
                                    13        23        33        43        53        63        73        83        93   |   103       113   |   123       133       143       153 
                                                                                                                   92-MSE|                 117-MSE                                 
                                                                                                                        97-MSE                                                     


Chain B from PDB  Type:PROTEIN  Length:155
 aligned with Q82X29_NITEU | Q82X29 from UniProtKB/TrEMBL  Length:166

    Alignment length:155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150     
         Q82X29_NITEU     1 MNEYFFPKLTAVEALAPYRLRTTWSTGEVLEVDVGDILRKIPDLAPILDPEAFARVHIAEWEGSVEWFDTEFGRDNVYAWAKEQAGEVSHEMFGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKIIPRTIWLACLGWEATRPETKTLPRTLPA 155
               SCOP domains d2auwb2 B:1-87 Hypothetical protein NE0471 N-terminal domain                           d2auwb1 B:88-155 Hypothetical protein NE0471 C-terminal domain       SCOP domains
               CATH domains -2auwB01 B:2-85 NE0471 N-terminal domain-like                                        2auwB02 B:86-155 lambda repressor-like DNA-binding domains             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee....eeeeee....eeeeehhhhhhhhhhhhhhhhhhhhh..ee......ee......hhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2auw B   1 mNEYFFPKLTAVEALAPYRLRTTWSTGEVLEVDVGDILRKIPDLAPILDPEAFARVHIAEWEGSVEWFDTEFGRDNVYAWAKEQAGEVSHEmFGDWmHRNNLSLTTAAEALGISRRmVSYYRTAHKIIPRTIWLACLGWEATRPETKTLPRTLPA 155
                            |       10        20        30        40        50        60        70        80        90 |    |100       110      |120       130       140       150     
                            1-MSE                                                                                     92-MSE|                 117-MSE                                  
                                                                                                                           97-MSE
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q82X29_NITEU | Q82X29)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

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