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(-) Description

Title :  CRYSTAL STRUCTURE OF A SUSD SUPERFAMILY PROTEIN (BDI_3964) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 1.95 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  13 Sep 10  (Deposition) - 03 Nov 10  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Putative Outer Membrane Protein, Susd, Carbohydrate Binding, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Susd Superfamily Protein (Bdi_3964) From Parabacteroides Distasonis Atcc 8503 At 1. 95 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUSD SUPERFAMILY 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: BDI_3964
    Organism Scientific: PARABACTEROIDES DISTASONIS
    Organism Taxid: 435591
    Strain: ATCC 8503
    Synonym: PUTATIVE OUTER MEMBRANE PROTEIN, PROBABLY INVOLVED IN NUTRIENT BINDING

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 55)

Asymmetric Unit (5, 55)
No.NameCountTypeFull Name
1ACT11Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3EDO24Ligand/Ion1,2-ETHANEDIOL
4MSE18Mod. Amino AcidSELENOMETHIONINE
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (4, 27)
No.NameCountTypeFull Name
1ACT7Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3EDO10Ligand/Ion1,2-ETHANEDIOL
4MSE9Mod. Amino AcidSELENOMETHIONINE
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (3, 27)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3EDO14Ligand/Ion1,2-ETHANEDIOL
4MSE9Mod. Amino AcidSELENOMETHIONINE
5PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 3 (4, 54)
No.NameCountTypeFull Name
1ACT11Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3EDO24Ligand/Ion1,2-ETHANEDIOL
4MSE18Mod. Amino AcidSELENOMETHIONINE
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (37, 37)

Asymmetric Unit (37, 37)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:168 , SER B:168 , HOH B:1136BINDING SITE FOR RESIDUE CL A 600
02AC2SOFTWAREASN A:268 , GLN A:278 , PHE A:279 , SER A:280 , ASN A:378BINDING SITE FOR RESIDUE ACT A 601
03AC3SOFTWARETRP A:107 , TYR A:111 , PRO A:161 , ILE A:163 , EDO A:625 , HOH A:640 , HOH A:1070BINDING SITE FOR RESIDUE ACT A 603
04AC4SOFTWAREASN A:136 , MSE A:139 , ALA A:140 , LYS A:143 , GLU A:194BINDING SITE FOR RESIDUE ACT A 604
05AC5SOFTWAREALA A:45 , ASN A:48 , HOH A:675 , ALA B:496BINDING SITE FOR RESIDUE ACT A 606
06AC6SOFTWARESER A:428 , GLU A:432 , EDO A:626 , HOH A:1133BINDING SITE FOR RESIDUE ACT A 607
07AC7SOFTWARESER A:318 , ARG A:459 , ASP A:461 , LYS A:462 , ACT A:609BINDING SITE FOR RESIDUE ACT A 608
08AC8SOFTWARESER A:318 , GLU A:320 , ARG A:459 , ACT A:608 , HOH A:1029BINDING SITE FOR RESIDUE ACT A 609
09AC9SOFTWAREVAL A:277 , GLN A:278 , ARG A:284 , HOH A:684 , HOH A:1146BINDING SITE FOR RESIDUE EDO A 612
10BC1SOFTWARELEU A:94 , LEU A:95 , VAL A:96 , TYR A:506 , HOH A:701 , HOH A:779BINDING SITE FOR RESIDUE EDO A 613
11BC2SOFTWARETYR A:111 , ILE A:163 , GLN A:167 , ACT A:603 , HOH A:638 , HOH A:865BINDING SITE FOR RESIDUE EDO A 625
12BC3SOFTWAREVAL A:396 , ALA A:427 , SER A:428 , ACT A:607BINDING SITE FOR RESIDUE EDO A 626
13BC4SOFTWARETHR A:334 , ASN A:335 , ASP A:354 , HOH A:1248BINDING SITE FOR RESIDUE EDO A 627
14BC5SOFTWARELEU A:281 , ASN A:282 , ASP A:376 , HOH B:1310BINDING SITE FOR RESIDUE EDO A 628
15BC6SOFTWAREASN A:503 , GLN A:504 , HOH A:688 , HOH A:1291 , GLN B:504 , HOH B:1091BINDING SITE FOR RESIDUE EDO A 630
16BC7SOFTWAREASN A:118 , ARG A:146 , THR A:164 , HOH A:851BINDING SITE FOR RESIDUE EDO A 631
17BC8SOFTWARETYR A:384 , GLN A:405 , GLN A:412BINDING SITE FOR RESIDUE EDO A 632
18BC9SOFTWAREASN A:48 , HOH A:1048BINDING SITE FOR RESIDUE EDO A 634
19CC1SOFTWAREGLN A:495 , HOH A:694 , HOH A:807 , HOH A:832 , HOH A:898 , HOH A:1031 , ARG B:284BINDING SITE FOR RESIDUE PEG A 636
20CC2SOFTWARELYS B:181 , TYR B:225 , GLY B:232 , TYR B:236BINDING SITE FOR RESIDUE ACT B 602
21CC3SOFTWAREASN B:136 , LYS B:143 , GLU B:194BINDING SITE FOR RESIDUE ACT B 605
22CC4SOFTWAREGLN A:174 , ALA A:496 , PRO A:498 , ALA B:45 , ASN B:48 , HOH B:939BINDING SITE FOR RESIDUE ACT B 610
23CC5SOFTWARESER B:428 , GLU B:432 , TRP B:435BINDING SITE FOR RESIDUE ACT B 611
24CC6SOFTWARELEU B:94 , LEU B:95 , VAL B:96 , HOH B:912BINDING SITE FOR RESIDUE EDO B 614
25CC7SOFTWAREPRO B:161 , LYS B:162 , VAL B:175 , SER B:176 , HOH B:1275BINDING SITE FOR RESIDUE EDO B 615
26CC8SOFTWAREASP A:354 , ASP B:185 , ILE B:189 , TYR B:225 , TYR B:236 , HOH B:964 , HOH B:1320BINDING SITE FOR RESIDUE EDO B 616
27CC9SOFTWAREASN B:48 , HOH B:1107BINDING SITE FOR RESIDUE EDO B 617
28DC1SOFTWAREVAL B:277 , GLN B:278 , ARG B:284 , HOH B:775BINDING SITE FOR RESIDUE EDO B 618
29DC2SOFTWARESER B:280 , LEU B:281 , ASN B:282 , ASP B:376 , HOH B:1474 , HOH B:1476BINDING SITE FOR RESIDUE EDO B 619
30DC3SOFTWAREILE B:310 , PRO B:311 , GLY B:357 , TYR B:358 , HOH B:1391BINDING SITE FOR RESIDUE EDO B 620
31DC4SOFTWARETHR B:326 , GLU B:328BINDING SITE FOR RESIDUE EDO B 621
32DC5SOFTWARETRP B:107 , TYR B:111 , HOH B:801BINDING SITE FOR RESIDUE EDO B 622
33DC6SOFTWAREHIS B:205 , GLU B:252 , THR B:254 , GLY B:271BINDING SITE FOR RESIDUE EDO B 623
34DC7SOFTWARETYR B:74 , MSE B:75 , GLY B:77 , ALA B:79 , TYR B:88 , PHE B:91 , LEU B:94 , TRP B:476 , TYR B:480 , HOH B:878 , HOH B:1049BINDING SITE FOR RESIDUE EDO B 624
35DC8SOFTWAREVAL B:396 , ASN B:397 , GLY B:400 , SER B:428BINDING SITE FOR RESIDUE EDO B 629
36DC9SOFTWAREASN B:371BINDING SITE FOR RESIDUE EDO B 633
37EC1SOFTWAREASN B:118 , GLN B:122 , ARG B:146 , THR B:164BINDING SITE FOR RESIDUE EDO B 635

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:228 -Pro A:229
2Tyr B:228 -Pro B:229

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OTN)

(-) 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:471
 aligned with A6LIX4_PARD8 | A6LIX4 from UniProtKB/TrEMBL  Length:506

    Alignment length:471
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505 
         A6LIX4_PARD8    36 KLTSKESALALTNSAYLKNTVFNKMTPGWGCNTILLLEYMTGKATSENSQSNYKDFQDLLVSDRSLYIEDWWQDCYAGIANCNLALQKLGEFENLDASLVNGYMAEVKFMRALYYFYLVRIFGDVPKITTVQSELGELQVSRAPVKEIYDEIIIPDLLEAEQSDLAFSDHTGRVSMGAVKALLADVYLTYAGYPLQGGKSYYAESAKRSLEVIKSNEYTLFTDYESLRLPSQNNKGEFIYQVQFSLNKRHNESVRIFLPSRSGISAYDLEYGSLIPTKEFVESFEKGDKRTEEKQYFFTNYKGHPSKFSPGAAELEFMDLNGYYIYKFFDQVAVDNTAKSDLNWSVYRYTDVLLMYAEAQVNADGTPNQQSIDIVNQIRGRAGLAPFKQTNASAFLEEVWDQRYFDLCYENKMWFDMLRTRKIRDDKSGEYVDFIGYKTNWGKVYTETQLLFPIPLSERQANPNLTQNQGY 506
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh.ee....ee.hhhhh.....ee..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh........hhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh........hhhhhhhhhh....eeeee........hhhhhhh.................eehhhhhh.....hhhhh....eeeee..........hhhhh.eeeeeeee....hhhhhhh.......eeeeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...hhhhhhhhhheee......eee............hhhhhh...hhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3otn A  36 KLTSKESALALTNSAYLKNTVFNKmTPGWGCNTILLLEYmTGKATSENSQSNYKDFQDLLVSDRSLYIEDWWQDCYAGIANCNLALQKLGEFENLDASLVNGYmAEVKFmRALYYFYLVRIFGDVPKITTVQSELGELQVSRAPVKEIYDEIIIPDLLEAEQSDLAFSDHTGRVSmGAVKALLADVYLTYAGYPLQGGKSYYAESAKRSLEVIKSNEYTLFTDYESLRLPSQNNKGEFIYQVQFSLNKRHNESVRIFLPSRSGISAYDLEYGSLIPTKEFVESFEKGDKRTEEKQYFFTNYKGHPSKFSPGAAELEFmDLNGYYIYKFFDQVAVDNTAKSDLNWSVYRYTDVLLmYAEAQVNADGTPNQQSIDIVNQIRGRAGLAPFKQTNASAFLEEVWDQRYFDLCYENKmWFDmLRTRKIRDDKSGEYVDFIGYKTNWGKVYTETQLLFPIPLSERQANPNLTQNQGY 506
                                    45        55    |   65        75        85        95       105       115       125       135   |   145       155       165       175       185       195       205     | 215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385    |  395       405       415       425       435       445  |   |455       465       475       485       495       505 
                                                   60-MSE         75-MSE                                                         139-MSE |                                                               211-MSE                                                                                                                                       353-MSE                              390-MSE                                                   448-MSE                                                      
                                                                                                                                       145-MSE                                                                                                                                                                                                                                                                                                            452-MSE                                                  


Chain B from PDB  Type:PROTEIN  Length:471
 aligned with A6LIX4_PARD8 | A6LIX4 from UniProtKB/TrEMBL  Length:506

    Alignment length:471
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505 
         A6LIX4_PARD8    36 KLTSKESALALTNSAYLKNTVFNKMTPGWGCNTILLLEYMTGKATSENSQSNYKDFQDLLVSDRSLYIEDWWQDCYAGIANCNLALQKLGEFENLDASLVNGYMAEVKFMRALYYFYLVRIFGDVPKITTVQSELGELQVSRAPVKEIYDEIIIPDLLEAEQSDLAFSDHTGRVSMGAVKALLADVYLTYAGYPLQGGKSYYAESAKRSLEVIKSNEYTLFTDYESLRLPSQNNKGEFIYQVQFSLNKRHNESVRIFLPSRSGISAYDLEYGSLIPTKEFVESFEKGDKRTEEKQYFFTNYKGHPSKFSPGAAELEFMDLNGYYIYKFFDQVAVDNTAKSDLNWSVYRYTDVLLMYAEAQVNADGTPNQQSIDIVNQIRGRAGLAPFKQTNASAFLEEVWDQRYFDLCYENKMWFDMLRTRKIRDDKSGEYVDFIGYKTNWGKVYTETQLLFPIPLSERQANPNLTQNQGY 506
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) SusD-like_3-3otnB03 B:36-223                                                                                                                                                                -----------------------------------------------SusD-3otnB01 B:271-506                                                                                                                                                                                                                       Pfam domains (1)
           Pfam domains (2) SusD-like_3-3otnB04 B:36-223                                                                                                                                                                -----------------------------------------------SusD-3otnB02 B:271-506                                                                                                                                                                                                                       Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh........hhhhh.......ee..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh........hhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh....eeeee........hhhhhhh.................eehhhhhh.....hhhhh....eeee...........hhhhh..eeeeeee....hhhhhhh.......eeeeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...hhhhhhhhhheee......eee............hhhhhh...hhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3otn B  36 KLTSKESALALTNSAYLKNTVFNKmTPGWGCNTILLLEYmTGKATSENSQSNYKDFQDLLVSDRSLYIEDWWQDCYAGIANCNLALQKLGEFENLDASLVNGYmAEVKFmRALYYFYLVRIFGDVPKITTVQSELGELQVSRAPVKEIYDEIIIPDLLEAEQSDLAFSDHTGRVSmGAVKALLADVYLTYAGYPLQGGKSYYAESAKRSLEVIKSNEYTLFTDYESLRLPSQNNKGEFIYQVQFSLNKRHNESVRIFLPSRSGISAYDLEYGSLIPTKEFVESFEKGDKRTEEKQYFFTNYKGHPSKFSPGAAELEFmDLNGYYIYKFFDQVAVDNTAKSDLNWSVYRYTDVLLmYAEAQVNADGTPNQQSIDIVNQIRGRAGLAPFKQTNASAFLEEVWDQRYFDLCYENKmWFDmLRTRKIRDDKSGEYVDFIGYKTNWGKVYTETQLLFPIPLSERQANPNLTQNQGY 506
                                    45        55    |   65        75        85        95       105       115       125       135   |   145       155       165       175       185       195       205     | 215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385    |  395       405       415       425       435       445  |   |455       465       475       485       495       505 
                                                   60-MSE         75-MSE                                                         139-MSE |                                                               211-MSE                                                                                                                                       353-MSE                              390-MSE                                                   448-MSE                                                      
                                                                                                                                       145-MSE                                                                                                                                                                                                                                                                                                            452-MSE
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 3OTN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: TPR (230)

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