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(-) Description

Title :  CRYSTAL STRUCTURE OF NGO0477 FROM NEISSERIA GONORRHOEAE
 
Authors :  J. Ren, S. Sainsbury, J. E. Nettleship, R. J. Owens, Oxford Protein Pr Facility (Oppf)
Date :  02 Dec 09  (Deposition) - 19 Jan 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Ngo0477, Neisseria Gonorrhoeae, New Protein Fold, Oppf, Structural Genomics, Oxford Protein Production Facility, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Ren, S. Sainsbury, J. E. Nettleship, N. J. Saunders, R. J. Owens
The Crystal Structure Of Ngo0477 From Neisseria Gonorrhoeae Reveals A Novel Protein Fold Incorporating A Helix-Turn-Helix Motif.
Proteins V. 78 1798 2010
PubMed-ID: 20196080  |  Reference-DOI: 10.1002/PROT.22698

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: OPPF1366
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES IN UNP 13-145
    Gene: NGO0477
    Organism Scientific: NEISSERIA GONORRHOEAE
    Organism Taxid: 242231
    Strain: FA1090
    Synonym: NGO0477 PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 51)

Asymmetric Unit (4, 51)
No.NameCountTypeFull Name
1ASN4Mod. Amino AcidASPARAGINE
2CL13Ligand/IonCHLORIDE ION
3MSE12Mod. Amino AcidSELENOMETHIONINE
4UNX22Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (3, 19)
No.NameCountTypeFull Name
1ASN2Mod. Amino AcidASPARAGINE
2CL-1Ligand/IonCHLORIDE ION
3MSE6Mod. Amino AcidSELENOMETHIONINE
4UNX11Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (3, 19)
No.NameCountTypeFull Name
1ASN2Mod. Amino AcidASPARAGINE
2CL-1Ligand/IonCHLORIDE ION
3MSE6Mod. Amino AcidSELENOMETHIONINE
4UNX11Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:7 , LEU A:9 , LYS A:16 , VAL A:18BINDING SITE FOR RESIDUE ASN A 140
02AC2SOFTWARELEU B:9 , LYS B:16 , VAL B:18 , LYS B:19BINDING SITE FOR RESIDUE ASN B 140
03AC3SOFTWARELYS C:7 , LEU C:9 , LYS C:16 , CYS C:17 , VAL C:18 , LYS C:19BINDING SITE FOR RESIDUE ASN C 140
04AC4SOFTWARELEU D:9 , LYS D:16 , VAL D:18 , LYS D:19BINDING SITE FOR RESIDUE ASN D 140
05AC5SOFTWARELYS A:42BINDING SITE FOR RESIDUE CL A 134
06AC6SOFTWAREMSE A:70BINDING SITE FOR RESIDUE CL A 135
07AC7SOFTWARELEU A:117 , ASN C:110BINDING SITE FOR RESIDUE CL A 136
08AC8SOFTWAREMSE A:130 , LYS D:7BINDING SITE FOR RESIDUE CL A 137
09AC9SOFTWAREARG A:92 , SER A:96BINDING SITE FOR RESIDUE CL A 138
10BC1SOFTWARELYS B:7 , MSE C:130BINDING SITE FOR RESIDUE CL B 134
11BC2SOFTWAREMSE B:70BINDING SITE FOR RESIDUE CL B 135
12BC3SOFTWAREMSE C:70BINDING SITE FOR RESIDUE CL C 134
13BC4SOFTWAREASN A:110 , LEU C:117BINDING SITE FOR RESIDUE CL C 135
14BC5SOFTWAREMSE D:70BINDING SITE FOR RESIDUE CL C 136
15BC6SOFTWARELYS C:42BINDING SITE FOR RESIDUE CL C 137
16BC7SOFTWAREARG C:92BINDING SITE FOR RESIDUE CL C 138
17BC8SOFTWARELYS C:97 , GLN C:98 , SER C:99BINDING SITE FOR RESIDUE CL C 139

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:8 -A:17
2B:8 -B:17
3C:8 -C:17
4D:8 -D:17

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KXA)

(-) 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:132
 aligned with Q5F9C2_NEIG1 | Q5F9C2 from UniProtKB/TrEMBL  Length:153

    Alignment length:134
                                                                                                                                                              153 
                                    30        40        50        60        70        80        90       100       110       120       130       140       150  | 
         Q5F9C2_NEIG1    21 IPVTHIKCLRINGQIKCVKPISPNTTPAAEHIEHVRKNPRRKAAMDRAAARIADKIALKAGGETFVSLRMKKGFTQSELATAAGLPQPYLSRIENSKQSLQDKTVQKLANALGVSPLEVRAAFERRYEYMEQA-   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....ee.........hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhh..hhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhhhhhhh....--. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kxa A   1 IPVTHIKCLRINGQIKCVKPISPNTTPAAEHIEHVRKNPRRKAAmDRAAARIADKIALKAGGETFVSLRmKKGFTQSELATAAGLPQPYLSRIENSKQSLQDKTVQKLANALGVSPLEVRAAFERRYEYmE--N 140
                                    10        20        30        40    |   50        60        70        80        90       100       110       120       130|  |
                                                                       45-MSE                   70-MSE                                                     130-MSE
                                                                                                                                                            131  |
                                                                                                                                                               140


Chain B from PDB  Type:PROTEIN  Length:131
 aligned with Q5F9C2_NEIG1 | Q5F9C2 from UniProtKB/TrEMBL  Length:153

    Alignment length:131
                                    30        40        50        60        70        80        90       100       110       120       130       140       150 
         Q5F9C2_NEIG1    21 IPVTHIKCLRINGQIKCVKPISPNTTPAAEHIEHVRKNPRRKAAMDRAAARIADKIALKAGGETFVSLRMKKGFTQSELATAAGLPQPYLSRIENSKQSLQDKTVQKLANALGVSPLEVRAAFERRYEYME 151
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....ee.........hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhh..hhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kxa B   1 IPVTHIKCLRINGQIKCVKPISPNTTPAAEHIEHVRKNPRRKAAmDRAAARIADKIALKAGGETFVSLRmKKGFTQSELATAAGLPQPYLSRIENSKQSLQDKTVQKLANALGVSPLEVRAAFERRYEYmN 140
                                    10        20        30        40    |   50        60        70        80        90       100       110       120       130|
                                                                       45-MSE                   70-MSE                                                     130-MSE
                                                                                                                                                            140


Chain C from PDB  Type:PROTEIN  Length:132
 aligned with Q5F9C2_NEIG1 | Q5F9C2 from UniProtKB/TrEMBL  Length:153

    Alignment length:132
                                    30        40        50        60        70        80        90       100       110       120       130       140       150  
         Q5F9C2_NEIG1    21 IPVTHIKCLRINGQIKCVKPISPNTTPAAEHIEHVRKNPRRKAAMDRAAARIADKIALKAGGETFVSLRMKKGFTQSELATAAGLPQPYLSRIENSKQSLQDKTVQKLANALGVSPLEVRAAFERRYEYMEQ 152
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee....ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhh..hhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhhhhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kxa C   1 IPVTHIKCLRINGQIKCVKPISPNTTPAAEHIEHVRKNPRRKAAmDRAAARIADKIALKAGGETFVSLRmKKGFTQSELATAAGLPQPYLSRIENSKQSLQDKTVQKLANALGVSPLEVRAAFERRYEYmEN 140
                                    10        20        30        40    |   50        60        70        80        90       100       110       120       130||
                                                                       45-MSE                   70-MSE                                                     130-MSE
                                                                                                                                                            131|
                                                                                                                                                             140


Chain D from PDB  Type:PROTEIN  Length:131
 aligned with Q5F9C2_NEIG1 | Q5F9C2 from UniProtKB/TrEMBL  Length:153

    Alignment length:131
                                    30        40        50        60        70        80        90       100       110       120       130       140       150 
         Q5F9C2_NEIG1    21 IPVTHIKCLRINGQIKCVKPISPNTTPAAEHIEHVRKNPRRKAAMDRAAARIADKIALKAGGETFVSLRMKKGFTQSELATAAGLPQPYLSRIENSKQSLQDKTVQKLANALGVSPLEVRAAFERRYEYME 151
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------HTH_3-3kxaD01 D:59-111                               -------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------HTH_3-3kxaD02 D:59-111                               -------------------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------HTH_3-3kxaD03 D:59-111                               -------------------- Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------HTH_3-3kxaD04 D:59-111                               -------------------- Pfam domains (4)
         Sec.struct. author ...eeeeeee....ee.........hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhh..hhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kxa D   1 IPVTHIKCLRINGQIKCVKPISPNTTPAAEHIEHVRKNPRRKAAmDRAAARIADKIALKAGGETFVSLRmKKGFTQSELATAAGLPQPYLSRIENSKQSLQDKTVQKLANALGVSPLEVRAAFERRYEYmN 140
                                    10        20        30        40    |   50        60        70        80        90       100       110       120       130|
                                                                       45-MSE                   70-MSE                                                     130-MSE
                                                                                                                                                            140
   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 3KXA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q5F9C2_NEIG1 | Q5F9C2)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.

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