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(-) Description

Title :  CRYSTAL STRUCTURE OF A DINB FAMILY MEMBER PROTEIN (SDEN_0562) FROM SHEWANELLA DENITRIFICANS AT 1.83 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  31 Jan 07  (Deposition) - 13 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Hypothetical Protein (Yp_561575. 1) Fro Shewanella Denitrificans Os-217 At 1. 83 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN
    Atcc: BAA-1090
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YP_561575.1, SDEN_0562
    Organism Scientific: SHEWANELLA DENITRIFICANS
    Organism Taxid: 192073
    Strain: OS217, DSM 15013

 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, 58)

Asymmetric Unit (4, 58)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO17Ligand/Ion1,2-ETHANEDIOL
3FMT24Ligand/IonFORMIC ACID
4MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 33)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO10Ligand/Ion1,2-ETHANEDIOL
3FMT15Ligand/IonFORMIC ACID
4MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (3, 24)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO7Ligand/Ion1,2-ETHANEDIOL
3FMT9Ligand/IonFORMIC ACID
4MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (38, 38)

Asymmetric Unit (38, 38)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG D:42 , ASN D:49 , EDO D:179BINDING SITE FOR RESIDUE CL D 174
02AC2SOFTWAREALA A:111 , THR A:126 , TYR A:128 , HOH A:320BINDING SITE FOR RESIDUE EDO A 174
03AC3SOFTWAREILE A:132 , GLU A:133 , ASP B:4 , VAL B:8 , HOH B:188BINDING SITE FOR RESIDUE EDO A 175
04AC4SOFTWARELEU A:5 , GLN A:9 , PHE A:10 , ILE A:136 , TYR A:140 , ILE B:132 , ILE B:136BINDING SITE FOR RESIDUE EDO A 176
05AC5SOFTWAREASN A:18 , ASP A:22 , ARG A:89 , HOH A:199 , HOH A:256BINDING SITE FOR RESIDUE EDO A 177
06AC6SOFTWAREGLY B:0 , ASP B:4 , HOH B:270BINDING SITE FOR RESIDUE EDO B 174
07AC7SOFTWAREILE A:132 , ILE A:136 , PRO A:137 , LEU B:5 , GLN B:9 , PHE B:10 , TYR B:140BINDING SITE FOR RESIDUE EDO B 175
08AC8SOFTWAREHIS A:152 , LEU B:43 , ALA B:44 , HOH B:191 , HOH B:196 , HIS C:152 , ASN C:153 , HOH C:185BINDING SITE FOR RESIDUE EDO B 176
09AC9SOFTWAREASN B:153 , GLY B:154 , HOH B:248 , ALA C:44 , ALA C:45 , ARG D:151 , HIS D:152 , GLY D:154 , EDO D:175BINDING SITE FOR RESIDUE EDO B 177
10BC1SOFTWAREVAL B:37 , ASN B:40 , SER B:41 , EDO B:179 , HOH B:235 , ASN C:40 , ARG C:42BINDING SITE FOR RESIDUE EDO B 178
11BC2SOFTWARESER B:41 , ARG B:42 , HIS B:152 , ASN B:153 , EDO B:178 , HOH C:207BINDING SITE FOR RESIDUE EDO B 179
12BC3SOFTWAREHIS A:152 , ASN A:153 , HOH A:198 , HIS C:152 , HOH C:183 , HOH C:186 , HOH C:240 , LEU D:43 , ALA D:44BINDING SITE FOR RESIDUE EDO C 174
13BC4SOFTWARELEU C:5 , GLN C:9 , PHE C:10 , ILE C:136 , TYR C:140 , ILE D:132 , ILE D:136BINDING SITE FOR RESIDUE EDO C 175
14BC5SOFTWAREALA A:44 , ALA A:45 , ARG B:151 , HIS B:152 , GLY B:154 , EDO B:177 , ASN D:153 , HOH D:277BINDING SITE FOR RESIDUE EDO D 175
15BC6SOFTWAREILE C:132 , ILE C:136 , LEU D:5 , GLN D:9 , PHE D:10 , TYR D:140BINDING SITE FOR RESIDUE EDO D 176
16BC7SOFTWAREGLN D:71 , TYR D:98 , GLY D:101BINDING SITE FOR RESIDUE EDO D 177
17BC8SOFTWARESER D:41 , ARG D:42 , HIS D:152 , ASN D:153 , HOH D:216BINDING SITE FOR RESIDUE EDO D 178
18BC9SOFTWAREVAL A:37 , ARG D:42 , PHE D:48 , CL D:174 , HOH D:217 , HOH D:231BINDING SITE FOR RESIDUE EDO D 179
19CC1SOFTWAREASN A:40 , ARG A:42 , HOH A:235 , VAL D:37BINDING SITE FOR RESIDUE FMT A 178
20CC2SOFTWAREGLN A:71 , PHE A:102 , ASP A:106 , HOH A:248BINDING SITE FOR RESIDUE FMT A 179
21CC3SOFTWAREASP A:4 , HOH A:193BINDING SITE FOR RESIDUE FMT A 181
22CC4SOFTWAREASP A:36 , ASN A:40 , HOH A:196 , HOH A:332 , HOH D:201BINDING SITE FOR RESIDUE FMT A 182
23CC5SOFTWAREGLN A:71 , THR A:74 , ALA A:75 , TYR A:98BINDING SITE FOR RESIDUE FMT A 183
24CC6SOFTWAREASP A:59 , HOH A:267BINDING SITE FOR RESIDUE FMT A 184
25CC7SOFTWARELYS A:12 , ASN A:16 , GLY A:164 , ALA A:165 , HOH A:259 , HOH A:276BINDING SITE FOR RESIDUE FMT A 185
26CC8SOFTWAREALA A:108 , ALA A:111BINDING SITE FOR RESIDUE FMT A 186
27CC9SOFTWAREGLN A:47 , TYR B:147 , ARG B:151 , FMT B:185 , HOH B:201BINDING SITE FOR RESIDUE FMT B 180
28DC1SOFTWARELYS B:23 , PHE B:27 , VAL B:155 , GLU B:156BINDING SITE FOR RESIDUE FMT B 182
29DC2SOFTWARELYS B:12 , ASN B:16 , GLY B:164 , ALA B:165BINDING SITE FOR RESIDUE FMT B 183
30DC3SOFTWARETHR B:84BINDING SITE FOR RESIDUE FMT B 184
31DC4SOFTWAREPHE A:48 , PHE A:141 , HIS A:142 , LYS B:159 , FMT B:180 , HOH B:189BINDING SITE FOR RESIDUE FMT B 185
32DC5SOFTWARELYS C:23 , ASP C:161BINDING SITE FOR RESIDUE FMT C 176
33DC6SOFTWAREGLU C:133 , HOH D:192BINDING SITE FOR RESIDUE FMT C 177
34DC7SOFTWAREGLN C:71 , GLY C:101 , HOH C:230BINDING SITE FOR RESIDUE FMT C 179
35DC8SOFTWARELYS C:23 , PHE C:27 , VAL C:155 , GLU C:156BINDING SITE FOR RESIDUE FMT C 180
36DC9SOFTWAREASP A:4 , GLU A:104BINDING SITE FOR RESIDUE FMT D 181
37EC1SOFTWARELYS B:31 , ASP C:46 , HOH C:219 , ARG D:151 , GLY D:154 , VAL D:155BINDING SITE FOR RESIDUE FMT D 182
38EC2SOFTWAREALA D:111 , THR D:126BINDING SITE FOR RESIDUE FMT D 183

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OQM)

(-) 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:180
 aligned with Q12RS4_SHEDO | Q12RS4 from UniProtKB/TrEMBL  Length:173

    Alignment length:180
                                     1                                                                                                                                                                          
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
         Q12RS4_SHEDO     - ---------MLYDLTVVQFSKMLKNLNAIFDKAEAFAELKKVDMDVLLNSRLAADQFNLIRQVQIACDTAKVGVARLTGQLETAPKHDDSETTLAELRQRIASVLTYLEGFSEADFANAATIQISQPRWQGKYLTGYEFAIEHAIPNLYFHITTAYGILRHNGVEVGKKDYLGAMPYKAP 171
               SCOP domains ---------d2oqma1 A:1-171 Hypothetical protein Sden0562                                                                                                                               SCOP domains
               CATH domains 2oqmA01 A:-8-164 dinb family like domain                                                                                                                                     ------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh........hhhhhhhhhhhhhhhhhhhhh.hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh.....ee.........eehhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2oqm A  -8 HHENLYFQGmLYDLTVVQFSKmLKNLNAIFDKAEAFAELKKVDmDVLLNSRLAADQFNLIRQVQIACDTAKVGVARLTGQLETAPKHDDSETTLAELRQRIASVLTYLEGFSEADFANAATIQISQPRWQGKYLTGYEFAIEHAIPNLYFHITTAYGILRHNGVEVGKKDYLGAmPYKAP 171
                                     1        11 |      21        31   |    41        51        61        71        81        91       101       111       121       131       141       151       161    |  171
                                     1-MSE      13-MSE                35-MSE                                                                                                                            166-MSE 


Chain B from PDB  Type:PROTEIN  Length:178
 aligned with Q12RS4_SHEDO | Q12RS4 from UniProtKB/TrEMBL  Length:173

    Alignment length:178
                                 1                                                                                                                                                                            
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165        
         Q12RS4_SHEDO     - -----MLYDLTVVQFSKMLKNLNAIFDKAEAFAELKKVDMDVLLNSRLAADQFNLIRQVQIACDTAKVGVARLTGQLETAPKHDDSETTLAELRQRIASVLTYLEGFSEADFANAATIQISQPRWQGKYLTGYEFAIEHAIPNLYFHITTAYGILRHNGVEVGKKDYLGAMPYKAPIL 173
               SCOP domains d2oqmb_ B: Hypothetical protein Sden0562                                                                                                                                           SCOP domains
               CATH domains 2oqmB01 B:-4-164 dinb family like domain                                                                                                                                 --------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh........hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh.....ee.hhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oqm B  -4 LYFQGmLYDLTVVQFSKmLKNLNAIFDKAEAFAELKKVDmDVLLNSRLAADQFNLIRQVQIACDTAKVGVARLTGQLETAPKHDDSETTLAELRQRIASVLTYLEGFSEADFANAATIQISQPRWQGKYLTGYEFAIEHAIPNLYFHITTAYGILRHNGVEVGKKDYLGAmPYKAPIL 173
                                 |   5       |15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165|       
                                 1-MSE      13-MSE                35-MSE                                                                                                                            166-MSE   


Chain C from PDB  Type:PROTEIN  Length:179
 aligned with Q12RS4_SHEDO | Q12RS4 from UniProtKB/TrEMBL  Length:173

    Alignment length:179
                                  1                                                                                                                                                                            
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164         
         Q12RS4_SHEDO     - ------MLYDLTVVQFSKMLKNLNAIFDKAEAFAELKKVDMDVLLNSRLAADQFNLIRQVQIACDTAKVGVARLTGQLETAPKHDDSETTLAELRQRIASVLTYLEGFSEADFANAATIQISQPRWQGKYLTGYEFAIEHAIPNLYFHITTAYGILRHNGVEVGKKDYLGAMPYKAPIL 173
               SCOP domains d2oqmc_ C: Hypothetical protein Sden0562                                                                                                                                            SCOP domains
               CATH domains 2oqmC01 C:-5-164 dinb family like domain                                                                                                                                  --------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh........hhhhhhhhhhhhhhhhhhhhh.hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh.....ee.hhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oqm C  -5 NLYFQGmLYDLTVVQFSKmLKNLNAIFDKAEAFAELKKVDmDVLLNSRLAADQFNLIRQVQIACDTAKVGVARLTGQLETAPKHDDSETTLAELRQRIASVLTYLEGFSEADFANAATIQISQPRWQGKYLTGYEFAIEHAIPNLYFHITTAYGILRHNGVEVGKKDYLGAmPYKAPIL 173
                                  |  4        14        24        34|       44        54        64        74        84        94       104       114       124       134       144       154       164 |       
                                  1-MSE      13-MSE                35-MSE                                                                                                                            166-MSE   


Chain D from PDB  Type:PROTEIN  Length:178
 aligned with Q12RS4_SHEDO | Q12RS4 from UniProtKB/TrEMBL  Length:173

    Alignment length:178
                                   1                                                                                                                                                                          
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163        
         Q12RS4_SHEDO     - -------MLYDLTVVQFSKMLKNLNAIFDKAEAFAELKKVDMDVLLNSRLAADQFNLIRQVQIACDTAKVGVARLTGQLETAPKHDDSETTLAELRQRIASVLTYLEGFSEADFANAATIQISQPRWQGKYLTGYEFAIEHAIPNLYFHITTAYGILRHNGVEVGKKDYLGAMPYKAP 171
               SCOP domains d2oqmd_ D: Hypothetical protein Sden0562                                                                                                                                           SCOP domains
               CATH domains 2oqmD01 D:-6-164 dinb family like domain                                                                                                                                   ------- CATH domains
           Pfam domains (1) --------DUF1993-2oqmD01 D:2-164                                                                                                                                            ------- Pfam domains (1)
           Pfam domains (2) --------DUF1993-2oqmD02 D:2-164                                                                                                                                            ------- Pfam domains (2)
           Pfam domains (3) --------DUF1993-2oqmD03 D:2-164                                                                                                                                            ------- Pfam domains (3)
           Pfam domains (4) --------DUF1993-2oqmD04 D:2-164                                                                                                                                            ------- Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh........hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh.....ee.........eehhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oqm D  -6 ENLYFQGmLYDLTVVQFSKmLKNLNAIFDKAEAFAELKKVDmDVLLNSRLAADQFNLIRQVQIACDTAKVGVARLTGQLETAPKHDDSETTLAELRQRIASVLTYLEGFSEADFANAATIQISQPRWQGKYLTGYEFAIEHAIPNLYFHITTAYGILRHNGVEVGKKDYLGAmPYKAP 171
                                   | 3        13        23        33 |      43        53        63        73        83        93       103       113       123       133       143       153       163  |     
                                   1-MSE      13-MSE                35-MSE                                                                                                                            166-MSE
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: DinB (11)

(-) Gene Ontology  (0, 0)

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