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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GERBC PROTEIN
 
Authors :  Y. Li, B. Setlow, P. Setlow, B. Hao
Date :  24 May 10  (Deposition) - 04 Aug 10  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  B
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  B  (2x)
Biol. Unit 3:  B  (6x)
Keywords :  A Novel Fold, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Li, B. Setlow, P. Setlow, B. Hao
Crystal Structure Of The Gerbc Component Of A Bacillus Subtilis Spore Germinant Receptor.
J. Mol. Biol. V. 402 8 2010
PubMed-ID: 20654628  |  Reference-DOI: 10.1016/J.JMB.2010.07.018

(-) Compounds

Molecule 1 - SPORE GERMINATION PROTEIN B3
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: A MODIFIED PET15B VECTOR
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: GERBC, RESIDUES 25-374
    Gene: BSU35820, GERBC
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS
    Organism Taxid: 224308
    Strain: 168

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : B
Biological Unit 1 (1x): B
Biological Unit 2 (2x): B
Biological Unit 3 (6x): B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1CL9Ligand/IonCHLORIDE ION
2SO49Ligand/IonSULFATE ION
Biological Unit 1 (1, 9)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO49Ligand/IonSULFATE ION
Biological Unit 2 (1, 18)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO418Ligand/IonSULFATE ION
Biological Unit 3 (1, 54)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO454Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS B:307 , ARG B:310 , ASP B:311 , LYS B:318 , HOH B:384 , HOH B:396 , HOH B:401BINDING SITE FOR RESIDUE SO4 B 1
02AC2SOFTWAREHIS B:43 , GLN B:44 , TYR B:45 , ALA B:80 , VAL B:81 , HOH B:532BINDING SITE FOR RESIDUE SO4 B 2
03AC3SOFTWARESER B:93 , ASP B:94 , HIS B:95 , LYS B:97 , ARG B:125 , ARG B:126 , HOH B:411BINDING SITE FOR RESIDUE SO4 B 3
04AC4SOFTWAREHOH B:17 , HIS B:73 , PHE B:141 , THR B:142 , LYS B:143BINDING SITE FOR RESIDUE SO4 B 4
05AC5SOFTWAREARG B:125BINDING SITE FOR RESIDUE SO4 B 5
06AC6SOFTWARELYS B:104 , ASN B:108 , HIS B:247 , GLN B:285 , CL B:376 , HOH B:468BINDING SITE FOR RESIDUE SO4 B 6
07AC7SOFTWAREARG B:107 , VAL B:217 , GLY B:218 , THR B:243 , LYS B:245 , GLY B:246 , GLU B:322 , TYR B:323BINDING SITE FOR RESIDUE SO4 B 7
08AC8SOFTWARELYS B:87 , GLN B:113BINDING SITE FOR RESIDUE SO4 B 8
09AC9SOFTWAREHIS B:338 , PRO B:339 , ASP B:340 , TYR B:341BINDING SITE FOR RESIDUE SO4 B 9
10BC1SOFTWAREGLN B:184 , HOH B:501BINDING SITE FOR RESIDUE CL B 375
11BC2SOFTWARESO4 B:6BINDING SITE FOR RESIDUE CL B 376
12BC3SOFTWARETYR B:49 , LYS B:75 , GLU B:123BINDING SITE FOR RESIDUE CL B 377
13BC4SOFTWAREGLN B:28 , HOH B:533BINDING SITE FOR RESIDUE CL B 378
14BC5SOFTWAREARG B:178BINDING SITE FOR RESIDUE CL B 379
15BC6SOFTWAREHOH B:519BINDING SITE FOR RESIDUE CL B 380
16BC7SOFTWAREARG B:178BINDING SITE FOR RESIDUE CL B 382
17BC8SOFTWAREVAL B:81 , SER B:82 , HOH B:537BINDING SITE FOR RESIDUE CL B 383

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N54)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Lys B:169 -Ile B:170
2Met B:171 -Ile B:172
3Ile B:172 -Pro B:173
4Lys B:198 -Gly B:199
5Gly B:199 -Lys B:200
6Glu B:265 -Asn B:266
7Gln B:285 -Asn B:286
8Ser B:293 -Lys B:294

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N54)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N54)

(-) Exons   (0, 0)

(no "Exon" information available for 3N54)

(-) 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 B from PDB  Type:PROTEIN  Length:311
 aligned with GERBC_BACSU | P39571 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:344
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364    
          GERBC_BACSU    25 DIEQLSFARGLAIDETNDHQYKLTYQNLLPQSEDSQASGKPEFVNVTSHGKTILEAVSDVSIKDPPVYSDHLKVILLGEKLMRNQNVDQVLNHFIRDDELRRSSYLMAARGNAADVFTKGNPNQQQPMPSEKLIDLTTHSGYNGKIMIPLRIGRASVYSQNGYSYLIQAVKNEKGKAKYDGAGIIKRGSNKLVGFLSADETQTLSWVMGTIQGGVMPTTDKGHPITFEIKKSKTKIKPVIENGKPVFHISVKTKGILTEDQNPNENSFSKSYLHRLENIFEKKLERDVKQVMDKLQHEYKTDPVFLSDHIRIQHPDYWNKVKGHWDEIFSETDFKYDISFKIIN 368
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------      ------------------------------------------------------------------------------------                      ----------------------------------Spore_GerAC-3n54B01 B:203-368                                                                                                                                          Pfam domains
         Sec.struct. author .......eeeeeeee.....eeeeeeee....------..hhhh.eeeeeeeeee..hhhhhhh.........eeeehhhhhhhhhhhhhhhhhhhhhhh....eeeee.............----------------------......hhhhhhhhhhh...eeeeeeee....eeeeeeeee......eeeeehhhhhhhhhhhh......eeeeee..eeeeeeeeeeeeeeeeee....eeeeeeeeeeeeee....-----..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhhhhhhheeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n54 B  25 DIEQLSFARGLAIDETNDHQYKLTYQNLLPQS------GKPEFVNVTSHGKTILEAVSDVSIKDPPVYSDHLKVILLGEKLMRNQNVDQVLNHFIRDDELRRSSYLMAARGNAADVFTKGNP----------------------KIMIPLRIGRASVYSQNGYSYLIQAVKNEKGKAKYDGAGIIKRGSNKLVGFLSADETQTLSWVMGTIQGGVMPTTDKGHPITFEIKKSKTKIKPVIENGKPVFHISVKTKGILTEDQN-----FSKSYLHRLENIFEKKLERDVKQVMDKLQHEYKTDPVFLSDHIRIQHPDYWNKVKGHWDEIFSETDFKYDISFKIIN 368
                                    34        44        54 |      64        74        84        94       104       114       124       134       144 |       -         -    |  174       184       194       204       214       224       234       244       254       264       274       284 |     294       304       314       324       334       344       354       364    
                                                          56     63                                                                                146                    169                                                                                                                  286   292
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 3N54)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N54)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Spore_GerAC] (1)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain B   (GERBC_BACSU | P39571)
biological process
    GO:0009847    spore germination    The physiological and developmental changes that occur in a spore following release from dormancy up to the earliest signs of growth (e.g. emergence from a spore wall).
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  3n54
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