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(-) Description

Title :  THE CRYSTAL STRUCTURE OF ABC TRANSPORTER FROM RHODOPSEUDOMONAS PALUSTRIS
 
Authors :  Z. Zhang, S. K. Burley, S. Swaminathan, New York Sgx Research Cente Structural Genomics (Nysgxrc)
Date :  23 Jun 10  (Deposition) - 13 Oct 10  (Release) - 13 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Abc Transporter, Sgx, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, S. K. Burley, S. Swaminathan
The Crystal Structure Of Abc Transporter From Rhodopseudomonas Palustris
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - POSSIBLE SUBSTRATE BINDING PROTEIN OF ABC TRANSPORTER SYSTEM
    Chains: B, A, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: CODON+RIL STRATAGENE
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RPA4397
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS
    Organism Taxid: 1076

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): AB  
Biological Unit 3 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 40)

Asymmetric Unit (1, 40)
No.NameCountTypeFull Name
1MSE40Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 40)
No.NameCountTypeFull Name
1MSE40Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 20)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 20)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3NND)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NND)

(-) Cis Peptide Bonds  (11, 11)

Asymmetric Unit
No.Residues
1Gly B:89 -Thr B:90
2Glu B:113 -Pro B:114
3Pro B:210 -Gly B:211
4Gly A:89 -Thr A:90
5Glu A:113 -Pro A:114
6Pro A:210 -Gly A:211
7Gly C:89 -Thr C:90
8Glu C:113 -Pro C:114
9Gly D:89 -Thr D:90
10Glu D:113 -Pro D:114
11Pro D:210 -Gly D:211

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NND)

(-) 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:339
 aligned with Q6N1K8_RHOPA | Q6N1K8 from UniProtKB/TrEMBL  Length:388

    Alignment length:355
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367     
         Q6N1K8_RHOPA    18 DLKIALIYGKTGPLEAYAKQTETGLMMGLEYATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGKQGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDALKDKPGKKIIWVIWAGGGDPLTKLQDMDPKRYGIELSTGGNILPALAAYKRLPGMEGATYYYYDIPKNPINEWLVTEHQKRFNAPPDFFTAGGFSAAMAVVTAVQKAKSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDPAVAWAVLEPV 372
               SCOP domains d3nnda_ A: automated matches                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhhhhhh....ee..eeeeeeeee...hhhhhhhhhhhhhhh....eee...hhhhhhhhhhhhhh...eeee...----------...eee...hhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhh....eeeeee...----hhhhhhh.......eee................--.....eeeeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..eeee..eeeeee....eeee.eeeeeeehhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nnd A  14 DLKIALIYGKTGPLEAYAKQTETGLmmGLEYATKGTmTLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPA----------NRYIFRTGRNSSQDAISNAVAIGKQGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDALKDKPGKKIIWVIWA----PLTKLQDmDPKRYGIELSTGGNILPALAAYKRL--mEGATYYYYDIPKNPINEWLVTEHQKRFNAPPDFFTAGGFSAAmAVVTAVQKAKSTDTEKLIAAmEGmEFDTPKGKmVFRKEDHQALQSmYHFKVKVDPAVAWAVLEEG 368
                                    23        33     || 43      | 53        63        73        83        93       103       113 |       -  |    133       143       153       163       173       183       193       203       213      |  - |     233       243       253   |  |263       273       283       293       303       313       323|  |   333  |    343     | 353       363     
                                                    39-MSE     50-MSE                                                          115        126                                                                                           220  225      |                      257  |                                        303-MSE              324-MSE     336-MSE      349-MSE               
                                                     40-MSE                                                                                                                                                                                         232-MSE                     260-MSE                                                            327-MSE                                     


Chain B from PDB  Type:PROTEIN  Length:330
 aligned with Q6N1K8_RHOPA | Q6N1K8 from UniProtKB/TrEMBL  Length:388

    Alignment length:352
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367  
         Q6N1K8_RHOPA    18 DLKIALIYGKTGPLEAYAKQTETGLMMGLEYATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGKQGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDALKDKPGKKIIWVIWAGGGDPLTKLQDMDPKRYGIELSTGGNILPALAAYKRLPGMEGATYYYYDIPKNPINEWLVTEHQKRFNAPPDFFTAGGFSAAMAVVTAVQKAKSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDPAVAWAVL 369
               SCOP domains d3nndb_ B: automated matches                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhhhhhh....ee..eeeeeeeee...hhhhhhhhhhhhhhh....eee...hhhhhhhhhhhhhhh..eee....----------...ee....hhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhh..eeeeeeee..--....hhhhhhhhhhh....e-eeee...----hhhhhhh..-....................----......eeeeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..eeee..eeeee......eee.eeeeeeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nnd B  14 DLKIALIYGKTGPLEAYAKQTETGLmmGLEYATKGTmTLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPA----------NRYIFRTGRNSSQDAISNAVAIGKQGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPT--TDFTAVGQRLFDALKDKPGK-IIWVIWA----PLTKLQDmD-KRYGIELSTGGNILPALAAY----GmEGATYYYYDIPKNPINEWLVTEHQKRFNAPPDFFTAGGFSAAmAVVTAVQKAKSTDTEKLIAAmEGmEFDTPKGKmVFRKEDHQALQSmYHFKVKVDPAVAWAVL 365
                                    23        33     || 43      | 53        63        73        83        93       103       113 |       -  |    133       143       153       163       173       183      |193       203        |-|     |  - |     233 |     243       253|    ||263       273       283       293       303       313       323|  |   333  |    343     | 353       363  
                                                    39-MSE     50-MSE                                                          115        126                                                             190  |                212 |   220  225      || |                254  259|                                        303-MSE              324-MSE     336-MSE      349-MSE            
                                                     40-MSE                                                                                                                                                  193                  214               232-MSE                     260-MSE                                                            327-MSE                                  
                                                                                                                                                                                                                                                     233 |                                                                                                                                  
                                                                                                                                                                                                                                                       235                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:329
 aligned with Q6N1K8_RHOPA | Q6N1K8 from UniProtKB/TrEMBL  Length:388

    Alignment length:352
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367  
         Q6N1K8_RHOPA    18 DLKIALIYGKTGPLEAYAKQTETGLMMGLEYATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGKQGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDALKDKPGKKIIWVIWAGGGDPLTKLQDMDPKRYGIELSTGGNILPALAAYKRLPGMEGATYYYYDIPKNPINEWLVTEHQKRFNAPPDFFTAGGFSAAMAVVTAVQKAKSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDPAVAWAVL 369
               SCOP domains d3nndc_ C: automated matches                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhhhhhh....ee..eeeeeeeee...hhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhh....eee...----------...eee...hhhhhhhhhhhhhhh..eeeeeeee.-hhhhhhhhhhhhhh.....eeeeeeee..--..hhhhhhhhhhhhh....eeeeee.------hhhhhhhhhhhhh.eee.............----......eeeeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..eeee..eeeee......eee.eeeeeeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nnd C  14 DLKIALIYGKTGPLEAYAKQTETGLmmGLEYATKGTmTLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPA----------NRYIFRTGRNSSQDAISNAVAIGKQGVTIATLAQD-AFGRDGVAAFKEALAKTGATLATEEYVPT--TDFTAVGQRLFDALKDKPGKKIIWVI------PLTKLQDmDPKRYGIELSTGGNILPALAAY----GmEGATYYYYDIPKNPINEWLVTEHQKRFNAPPDFFTAGGFSAAmAVVTAVQKAKSTDTEKLIAAmEGmEFDTPKGKmVFRKEDHQALQSmYHFKVKVDPAVAWAVL 365
                                    23        33     || 43      | 53        63        73        83        93       103       113 |       -  |    133       143       153      |163       173       183      |193       203       213    |    - |     233       243       253|    ||263       273       283       293       303       313       323|  |   333  |    343     | 353       363  
                                                    39-MSE     50-MSE                                                          115        126                               160 |                         190  |                      218    225      |                   254  259|                                        303-MSE              324-MSE     336-MSE      349-MSE            
                                                     40-MSE                                                                                                                   162                            193                                    232-MSE                     260-MSE                                                            327-MSE                                  


Chain D from PDB  Type:PROTEIN  Length:328
 aligned with Q6N1K8_RHOPA | Q6N1K8 from UniProtKB/TrEMBL  Length:388

    Alignment length:352
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367  
         Q6N1K8_RHOPA    18 DLKIALIYGKTGPLEAYAKQTETGLMMGLEYATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGKQGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDALKDKPGKKIIWVIWAGGGDPLTKLQDMDPKRYGIELSTGGNILPALAAYKRLPGMEGATYYYYDIPKNPINEWLVTEHQKRFNAPPDFFTAGGFSAAMAVVTAVQKAKSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDPAVAWAVL 369
               SCOP domains d3nndd_ D: automated matches                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Peripla_BP_6-3nndD01 D:14-358                                                                                                                                                                                                                                                                                                                            ------- Pfam domains (1)
           Pfam domains (2) Peripla_BP_6-3nndD02 D:14-358                                                                                                                                                                                                                                                                                                                            ------- Pfam domains (2)
           Pfam domains (3) Peripla_BP_6-3nndD03 D:14-358                                                                                                                                                                                                                                                                                                                            ------- Pfam domains (3)
           Pfam domains (4) Peripla_BP_6-3nndD04 D:14-358                                                                                                                                                                                                                                                                                                                            ------- Pfam domains (4)
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhhhhhh....ee..eeeeeeeee...hhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhh...eee...----------...ee....hhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhh....eeeeeeee..-----.hhhhhhhhhhh....eeeeeee.-----hhhhhhhhhhhhh.eee..............----.....eeeeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..eeee..eeeee.hhhh.eee.eeeeeeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nnd D  14 DLKIALIYGKTGPLEAYAKQTETGLmmGLEYATKGTmTLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPA----------NRYIFRTGRNSSQDAISNAVAIGKQGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPT-----TAVGQRLFDALKDKPGKKIIWVIW-----PLTKLQDmDPKRYGIELSTGGNILPALAAYK----mEGATYYYYDIPKNPINEWLVTEHQKRFNAPPDFFTAGGFSAAmAVVTAVQKAKSTDTEKLIAAmEGmEFDTPKGKmVFRKEDHQALQSmYHFKVKVDPAVAWAVL 365
                                    23        33     || 43      | 53        63        73        83        93       103       113 |       -  |    133       143       153       163       173       183      |  -  |    203       213     |   - |     233       243       253 |    |263       273       283       293       303       313       323|  |   333  |    343     | 353       363  
                                                    39-MSE     50-MSE                                                          115        126                                                             190   196                    219   225      |                    255    |                                        303-MSE              324-MSE     336-MSE      349-MSE            
                                                     40-MSE                                                                                                                                                                                         232-MSE                     260-MSE                                                            327-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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Periplas_BP (97)

(-) Gene Ontology  (0, 0)

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