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(-) Description

Title :  CRYSTAL STRUCTURE OF A CALCIUM BINDING PROTEIN (BDI_1975) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 2.00 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  30 Sep 11  (Deposition) - 25 Jan 12  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Blip-Like, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Hypothetical Periplasmic Protein (Bdi_1975) From Parabacteroides Distasonis Atcc 8503 At 2. 0 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PERIPLASMIC PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: PB1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BDI_1975
    Organism Scientific: PARABACTEROIDES DISTASONIS
    Organism Taxid: 435591
    Strain: ATCC 8503

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 47)

Asymmetric Unit (5, 47)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2CA4Ligand/IonCALCIUM ION
3CL11Ligand/IonCHLORIDE ION
4EDO6Ligand/Ion1,2-ETHANEDIOL
5MSE21Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 19)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4EDO2Ligand/Ion1,2-ETHANEDIOL
5MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (3, 26)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4EDO8Ligand/Ion1,2-ETHANEDIOL
5MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:275 , HOH A:631 , HOH A:1116 , HOH A:1117 , HOH A:1122 , HOH A:1123 , HOH B:969BINDING SITE FOR RESIDUE CA A 279
02AC2SOFTWARESER A:104 , PHE A:105BINDING SITE FOR RESIDUE CL A 284
03AC3SOFTWAREGLN A:225 , ILE A:226 , ASN B:65BINDING SITE FOR RESIDUE CL A 285
04AC4SOFTWARESER A:260 , HIS A:261 , GLY A:263BINDING SITE FOR RESIDUE CL A 290
05AC5SOFTWAREPHE A:175 , LYS A:201 , HOH A:367 , HOH A:1025BINDING SITE FOR RESIDUE CL A 291
06AC6SOFTWAREARG A:119 , TYR A:140 , LYS A:149 , ASP A:182 , HOH A:371BINDING SITE FOR RESIDUE ACT A 293
07AC7SOFTWARETHR A:72 , LYS A:85BINDING SITE FOR RESIDUE ACT A 295
08AC8SOFTWAREASN B:275 , HOH B:956 , HOH B:1113 , HOH B:1114 , HOH B:1115BINDING SITE FOR RESIDUE CA B 280
09AC9SOFTWARESER B:260 , HIS B:261 , GLY B:263BINDING SITE FOR RESIDUE CL B 283
10BC1SOFTWARELYS B:201 , EDO B:301BINDING SITE FOR RESIDUE CL B 287
11BC2SOFTWARESER A:234 , ALA A:235 , ASN B:134 , SER B:135BINDING SITE FOR RESIDUE CL B 292
12BC3SOFTWAREARG B:119 , TYR B:140 , LYS B:149 , ASP B:182 , HOH B:659 , HOH B:782BINDING SITE FOR RESIDUE ACT B 297
13BC4SOFTWAREHOH A:1123 , GLU B:70 , THR B:72 , LYS B:85BINDING SITE FOR RESIDUE EDO B 299
14BC5SOFTWARETHR B:214 , CL B:287 , HOH C:807 , HOH C:1129BINDING SITE FOR RESIDUE EDO B 301
15BC6SOFTWAREASN C:275 , HOH C:748 , HOH C:1109 , HOH C:1110 , HOH C:1111 , HOH C:1112 , HOH C:1121BINDING SITE FOR RESIDUE CA C 278
16BC7SOFTWAREASP C:63 , HOH C:466 , HOH C:467 , HOH C:468 , HOH C:469 , HOH C:930BINDING SITE FOR RESIDUE CA C 281
17BC8SOFTWARELYS C:201 , EDO C:302BINDING SITE FOR RESIDUE CL C 282
18BC9SOFTWARESER C:260 , HIS C:261 , ASN C:262 , GLY C:263BINDING SITE FOR RESIDUE CL C 286
19CC1SOFTWARESER C:104 , PHE C:105 , GLN C:264 , HOH C:821BINDING SITE FOR RESIDUE CL C 288
20CC2SOFTWAREASN C:134 , SER C:135 , SER C:234 , ALA C:235 , HOH C:326BINDING SITE FOR RESIDUE CL C 289
21CC3SOFTWARELYS C:44 , GLU C:84 , HOH C:550BINDING SITE FOR RESIDUE ACT C 294
22CC4SOFTWAREARG C:119 , VAL C:125 , TYR C:140 , LYS C:149 , ASP C:182 , HOH C:336 , HOH C:764BINDING SITE FOR RESIDUE ACT C 296
23CC5SOFTWAREGLU C:70 , THR C:72 , LYS C:85 , HOH C:827 , HOH C:1049BINDING SITE FOR RESIDUE EDO C 298
24CC6SOFTWARESER C:260 , GLY C:263 , ASP C:265BINDING SITE FOR RESIDUE EDO C 300
25CC7SOFTWARETHR C:174 , PHE C:175 , THR C:214 , LEU C:248 , CL C:282BINDING SITE FOR RESIDUE EDO C 302
26CC8SOFTWAREASN C:146 , GLN C:198 , TYR C:200 , HOH C:734BINDING SITE FOR RESIDUE EDO C 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U1W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3U1W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U1W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3U1W)

(-) Exons   (0, 0)

(no "Exon" information available for 3U1W)

(-) 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:249
 aligned with A6LDE6_PARD8 | A6LDE6 from UniProtKB/TrEMBL  Length:277

    Alignment length:249
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268         
         A6LDE6_PARD8    29 QGIIPLPPVENAFQEKYPDAKNPVFEIEGNYYVVDFNNGGSETTAWFTDQGIWMMEKIDISFAQLPAAVSTAFKQSFYSNWTVDDTYAINRLNMGIVYKIEAEQSNSEVDLYYSQYGNLIKAVDDEINNDAPIVIPKEVSNLMEITFANAELLDIQQNSLGYELDMIDNQIYKVAQLNKDYRWQSTTWAMSEQEVPQIVMQGFESSAYASDKVQSIYTLLNANGTFYLFKVSHNGQDKTITFDVFGNIV 277
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh...eeeeeeee..eeeeeeee..eeeeeee.....eeeeeeeehhhhhhhhhhhhhhh......eeeeeeeeee.....eeeeeeee..eeeeeee.....eeeeee...........hhhhhhhhhhhh...eeeeeeee..eeeeeeee..eeeeeee.....eeeeeee.hhhhhhhhhhhhhhhhhhhhheeeeeeeeee..eeeeeeeeee..eeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u1w A  29 QGIIPLPPVENAFQEKYPDAKNPVFEIEGNYYVVDFNNGGSETTAWFTDQGIWmmEKIDISFAQLPAAVSTAFKQSFYSNWTVDDTYAINRLNmGIVYKIEAEQSNSEVDLYYSQYGNLIKAVDDEINNDAPIVIPKEVSNLmEITFANAELLDIQQNSLGYELDmIDNQIYKVAQLNKDYRWQSTTWAmSEQEVPQIVmQGFESSAYASDKVQSIYTLLNANGTFYLFKVSHNGQDKTITFDVFGNIV 277
                                    38        48        58        68        78   ||   88        98       108       118   |   128       138       148       158       168  |    178       188     | 198       208       218       228       238       248       258       268         
                                                                                82-MSE                                 122-MSE                                          171-MSE                194-MSE                 218-MSE   228-MSE                                             
                                                                                 83-MSE                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:249
 aligned with A6LDE6_PARD8 | A6LDE6 from UniProtKB/TrEMBL  Length:277

    Alignment length:249
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268         
         A6LDE6_PARD8    29 QGIIPLPPVENAFQEKYPDAKNPVFEIEGNYYVVDFNNGGSETTAWFTDQGIWMMEKIDISFAQLPAAVSTAFKQSFYSNWTVDDTYAINRLNMGIVYKIEAEQSNSEVDLYYSQYGNLIKAVDDEINNDAPIVIPKEVSNLMEITFANAELLDIQQNSLGYELDMIDNQIYKVAQLNKDYRWQSTTWAMSEQEVPQIVMQGFESSAYASDKVQSIYTLLNANGTFYLFKVSHNGQDKTITFDVFGNIV 277
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh...eeeeeeee..eeeeeeee..eeeeeee.....eeeeeeeehhhhhhhhhhhhhhh......eeeeeeeeee.....eeeeeeee..eeeeeee.....eeeeee...........hhhhhhhhhhhh...eeeeeeee..eeeeeeee..eeeeeee.....eeeeeee......hhhhhhhhhh......eeeeeeeeee..eeeeeeeeee..eeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u1w B  29 QGIIPLPPVENAFQEKYPDAKNPVFEIEGNYYVVDFNNGGSETTAWFTDQGIWmmEKIDISFAQLPAAVSTAFKQSFYSNWTVDDTYAINRLNmGIVYKIEAEQSNSEVDLYYSQYGNLIKAVDDEINNDAPIVIPKEVSNLmEITFANAELLDIQQNSLGYELDmIDNQIYKVAQLNKDYRWQSTTWAmSEQEVPQIVmQGFESSAYASDKVQSIYTLLNANGTFYLFKVSHNGQDKTITFDVFGNIV 277
                                    38        48        58        68        78   ||   88        98       108       118   |   128       138       148       158       168  |    178       188     | 198       208       218       228       238       248       258       268         
                                                                                82-MSE                                 122-MSE                                          171-MSE                194-MSE                 218-MSE   228-MSE                                             
                                                                                 83-MSE                                                                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:250
 aligned with A6LDE6_PARD8 | A6LDE6 from UniProtKB/TrEMBL  Length:277

    Alignment length:250
                                    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
         A6LDE6_PARD8    28 HQGIIPLPPVENAFQEKYPDAKNPVFEIEGNYYVVDFNNGGSETTAWFTDQGIWMMEKIDISFAQLPAAVSTAFKQSFYSNWTVDDTYAINRLNMGIVYKIEAEQSNSEVDLYYSQYGNLIKAVDDEINNDAPIVIPKEVSNLMEITFANAELLDIQQNSLGYELDMIDNQIYKVAQLNKDYRWQSTTWAMSEQEVPQIVMQGFESSAYASDKVQSIYTLLNANGTFYLFKVSHNGQDKTITFDVFGNIV 277
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh...eeeeeeee..eeeeeeee..eeeeeee.....eeeeeeeehhhhhhhhhhhhhhh......eeeeeeeeee.....eeeeeeee..eeeeeee.....eeeeee...........hhhhhhhhhhhh..eeeeeeeee..eeeeeeee..eeeeeee.....eeeeeeeehhhhhhhhhhhhhhh......eeeeeeeeee..eeeeeeeeee..eeeeeeee....ee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u1w C  28 HQGIIPLPPVENAFQEKYPDAKNPVFEIEGNYYVVDFNNGGSETTAWFTDQGIWmmEKIDISFAQLPAAVSTAFKQSFYSNWTVDDTYAINRLNmGIVYKIEAEQSNSEVDLYYSQYGNLIKAVDDEINNDAPIVIPKEVSNLmEITFANAELLDIQQNSLGYELDmIDNQIYKVAQLNKDYRWQSTTWAmSEQEVPQIVmQGFESSAYASDKVQSIYTLLNANGTFYLFKVSHNGQDKTITFDVFGNIV 277
                                    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
                                                                                 82-MSE                                 122-MSE                                          171-MSE                194-MSE                 218-MSE   228-MSE                                             
                                                                                  83-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  (0, 0)

(no "SCOP Domain" information available for 3U1W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U1W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U1W)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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