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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRIMERIC BACTERIAL MICROCOMPARTMENT SHELL PROTEIN PDUB WITH GLYCEROL METABOLITES
 
Authors :  A. H. Pang, M. B. Prentice, R. W. Pickersgill
Date :  22 May 12  (Deposition) - 21 Nov 12  (Release) - 12 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.56
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Bmc Domain, Shell Protein, Glycerol-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Pang, M. Liang, M. B. Prentice, R. W. Pickersgill
Substrate Channels Revealed In The Trimeric Lactobacillus Reuteri Bacterial Microcompartment Shell Protein Pdub.
Acta Crystallogr. , Sect. D V. 68 1642 2012
PubMed-ID: 23151629  |  Reference-DOI: 10.1107/S0907444912039315

(-) Compounds

Molecule 1 - MICROCOMPARTMENTS PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LREU_1748, PDUB
    Organism Scientific: LACTOBACILLUS REUTERI
    Organism Taxid: 557436
    Strain: DSM 20016

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric/Biological Unit (2, 18)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL17Ligand/IonGLYCEROL

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:80 , GLY A:189 , THR A:190 , SER A:191 , HOH A:525 , HOH A:531 , HOH C:418BINDING SITE FOR RESIDUE GOL A 301
02AC2SOFTWAREALA A:57 , GLY A:58 , HIS A:90 , GLU A:131 , GLU A:195 , CYS A:197 , GOL A:303 , HOH A:403BINDING SITE FOR RESIDUE GOL A 302
03AC3SOFTWAREGLY A:56 , ALA A:57 , PRO A:59 , GLY A:89 , HIS A:90 , GLU A:131 , GLU A:195 , GOL A:302 , GOL A:304BINDING SITE FOR RESIDUE GOL A 303
04AC4SOFTWARETHR A:55 , GLY A:87 , VAL A:122 , ASN A:124 , HIS A:129 , GOL A:303 , HOH A:506BINDING SITE FOR RESIDUE GOL A 304
05AC5SOFTWAREASP A:37 , LEU A:39 , HIS A:40 , LYS A:152 , HOH A:459 , HOH A:462 , HOH A:465 , HOH A:473BINDING SITE FOR RESIDUE GOL A 305
06AC6SOFTWAREARG A:82 , ASP A:83 , GLY A:86 , GLY A:87 , HOH A:434 , ARG B:82 , ASP B:83 , HOH B:419 , ARG C:82 , HOH C:452BINDING SITE FOR RESIDUE GOL A 306
07AC7SOFTWARELEU A:173 , LYS A:174 , ALA A:176 , ALA C:136 , ARG C:137 , HOH C:466BINDING SITE FOR RESIDUE GOL A 307
08AC8SOFTWAREHOH A:413 , TRP B:80 , GLY B:189 , THR B:190 , SER B:191BINDING SITE FOR RESIDUE GOL B 301
09AC9SOFTWAREALA B:57 , GLY B:58 , HIS B:90 , GLU B:131 , GLU B:195 , CYS B:197 , GOL B:303 , HOH B:417BINDING SITE FOR RESIDUE GOL B 302
10BC1SOFTWAREGLY B:56 , ALA B:57 , PRO B:59 , GLY B:89 , HIS B:90 , GLU B:131 , GLU B:195 , GOL B:302 , GOL B:304BINDING SITE FOR RESIDUE GOL B 303
11BC2SOFTWARETHR B:84 , GLY B:87 , VAL B:122 , ASN B:124 , HIS B:129 , GOL B:303 , HOH B:472BINDING SITE FOR RESIDUE GOL B 304
12BC3SOFTWAREHOH A:464 , ASP B:37 , LYS B:38 , LEU B:39 , HIS B:40 , HOH B:452BINDING SITE FOR RESIDUE GOL B 305
13BC4SOFTWAREALA A:136 , ARG A:137 , HOH A:432 , LEU B:173 , LYS B:174 , ALA B:176BINDING SITE FOR RESIDUE GOL B 306
14BC5SOFTWAREALA B:136 , ARG B:137 , HOH B:483 , LEU C:173 , LYS C:174 , ALA C:176BINDING SITE FOR RESIDUE ACT B 307
15BC6SOFTWAREHOH B:436 , TRP C:80 , GLY C:189 , THR C:190 , SER C:191 , HOH C:447 , HOH C:500BINDING SITE FOR RESIDUE GOL C 301
16BC7SOFTWAREALA C:57 , GLY C:58 , HIS C:90 , GLU C:131 , GLU C:195 , CYS C:197 , GOL C:303 , HOH C:406BINDING SITE FOR RESIDUE GOL C 302
17BC8SOFTWAREGLY C:56 , ALA C:57 , GLY C:58 , PRO C:59 , THR C:84 , GLY C:89 , HIS C:90 , GLU C:131 , GLU C:195 , GOL C:302 , GOL C:304BINDING SITE FOR RESIDUE GOL C 303
18BC9SOFTWARETHR C:55 , GLY C:87 , VAL C:122 , ASN C:124 , HIS C:129 , GOL C:303 , HOH C:455BINDING SITE FOR RESIDUE GOL C 304

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:158 -A:197
2B:158 -B:197
3C:158 -C:197

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Cys A:160 -Pro A:161
2Cys B:160 -Pro B:161
3Cys C:160 -Pro C:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FAY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FAY)

(-) Exons   (0, 0)

(no "Exon" information available for 4FAY)

(-) Sequences/Alignments

Asymmetric/Biological 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:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eeeeee...hhhhhh.........eeeeeee...hhhhhhhhhhhhhhh..eeeeee............eeeeeee.hhhhhhhhhhhhhhhhhhhh..eeee..eeeeeeee...hhhhhhhhh......eeeeeeehhhhhhhhhhhhhhhh..eeeeee...........eeeeee.hhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fay A  11 VPEFVGASEIGDTIGMVIPRVDQQLLDKLHVTKQYKTLGILSDRTGAGPQIMAMDEGIKATNMECIDVEWPRDTKGGGGHGCLIIIGGDDPADARQAIRVALDNLHRTFGDVYNAKAGHLELQFTARAAGAAHLGLGAVEGKAFGLICGCPSGIGVVMGDKALKTAGVEPLNFTSPSHGTSFSNEGCLTITGDSGAVRQAVMAGREVGLKLLSQFGEEPVNDFPSYI 237
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       


Chain B from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eeeeee...hhhhhhhh.......eeeeeee...hhhhhhhhhhhhhh...eeeeee...hhhhh....eeeeeee.hhhhhhhhhhhhhhhhhhhh..eeee..eeeeeeee...hhhhhhhhh......eeeeeee.hhhhhhhhhhhhhhh..eeeeee...........eeeeee.hhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fay B  11 VPEFVGASEIGDTIGMVIPRVDQQLLDKLHVTKQYKTLGILSDRTGAGPQIMAMDEGIKATNMECIDVEWPRDTKGGGGHGCLIIIGGDDPADARQAIRVALDNLHRTFGDVYNAKAGHLELQFTARAAGAAHLGLGAVEGKAFGLICGCPSGIGVVMGDKALKTAGVEPLNFTSPSHGTSFSNEGCLTITGDSGAVRQAVMAGREVGLKLLSQFGEEPVNDFPSYI 237
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       


Chain C from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eeeeee...hhhhhhhh.......eeeeeee...hhhhhhhhhhhhhh...eeeeee...hhhhh....eeeeeee.hhhhhhhhhhhhhhhhhhhh..eeee..eeeeeeee...hhhhhhhhh......eeeeeeehhhhhhhhhhhhhhhh..eeeeee...........eeeeee.hhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fay C  11 VPEFVGASEIGDTIGMVIPRVDQQLLDKLHVTKQYKTLGILSDRTGAGPQIMAMDEGIKATNMECIDVEWPRDTKGGGGHGCLIIIGGDDPADARQAIRVALDNLHRTFGDVYNAKAGHLELQFTARAAGAAHLGLGAVEGKAFGLICGCPSGIGVVMGDKALKTAGVEPLNFTSPSHGTSFSNEGCLTITGDSGAVRQAVMAGREVGLKLLSQFGEEPVNDFPSYI 237
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   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 4FAY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FAY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FAY)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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