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(-) Description

Title :  STRUCTURE OF LEPTOSPIRA INTERROGANS LRR PROTEIN LIC12759
 
Authors :  W. Shepard, F. A. Saul, A. Haouz, M. Picardeau
Date :  11 Jul 14  (Deposition) - 03 Jun 15  (Release) - 17 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lrr Protein, Pathogen, Virulence Factor, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Miras, F. Saul, M. Nowakowski, P. Weber, A. Haouz, W. Shepard, M. Picardeau
Structural Characterization Of A Novel Subfamily Of Leucine-Rich Repeat Proteins From The Human Pathogen Leptospira Interrogans.
Acta Crystallogr. , Sect. D V. 71 1351 2015
PubMed-ID: 26057675  |  Reference-DOI: 10.1107/S139900471500704X

(-) Compounds

Molecule 1 - LIC12759
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PDEST17
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector Type: PLASMID
    Gene: LIC_12759
    Organism Scientific: LEPTOSPIRA INTERROGANS SEROVAR COPENHAGENI STR. FIOCRUZ L1-130
    Organism Taxid: 267671
    Synonym: LIC12759

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 19)

Asymmetric Unit (6, 19)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2MES3Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MSE4Mod. Amino AcidSELENOMETHIONINE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5SO41Ligand/IonSULFATE ION
6ZN6Ligand/IonZINC ION
Biological Unit 1 (4, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MSE2Mod. Amino AcidSELENOMETHIONINE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5SO41Ligand/IonSULFATE ION
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MSE2Mod. Amino AcidSELENOMETHIONINE
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
5SO4-1Ligand/IonSULFATE ION
6ZN-1Ligand/IonZINC ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:369 , GLU A:392 , HIS B:303 , CL B:508binding site for residue ZN A 501
02AC2SOFTWAREHIS A:303 , GLY B:371 , ASP B:394 , CL B:505 , CL B:507binding site for residue ZN A 502
03AC3SOFTWAREGLU A:257 , GLU B:369 , CL B:506 , HOH B:681binding site for residue ZN A 503
04AC4SOFTWAREHIS A:188 , HOH A:666 , GLU B:343 , HOH B:693 , HOH B:713binding site for residue ZN A 504
05AC5SOFTWARELYS A:28 , TYR A:30 , LYS A:31 , ASN A:32 , HOH A:784binding site for residue MES A 505
06AC6SOFTWARETYR A:302 , HOH A:736 , TYR B:280 , CL B:508binding site for residue SO4 A 506
07AC7SOFTWARETYR A:302 , HIS A:323 , SER A:325 , SER A:346 , HOH A:730 , TYR B:280 , HOH B:728binding site for residue PEG A 507
08AC8SOFTWARESER B:162 , ASP B:185 , HOH B:791binding site for residue ZN B 501
09AC9SOFTWAREHOH A:662 , HOH A:694 , HOH A:730 , GLU B:257 , HOH B:727binding site for residue ZN B 502
10AD1SOFTWARETYR A:279 , HOH A:660 , TYR B:302 , HIS B:323 , SER B:325 , SER B:346 , HOH B:710 , HOH B:728 , HOH B:732 , HOH B:739binding site for residue MES B 503
11AD2SOFTWARELYS A:401 , LYS B:28 , TYR B:30 , LYS B:31 , ASN B:32 , LYS B:35 , HOH B:619binding site for residue MES B 504
12AD3SOFTWARETYR A:280 , HIS A:303 , ZN A:502 , GLY B:371 , GLU B:392 , ASP B:394 , CL B:507binding site for residue CL B 505
13AD4SOFTWAREGLU A:257 , ZN A:503 , ARG B:367 , LEU B:368 , GLU B:369 , ARG B:390binding site for residue CL B 506
14AD5SOFTWAREZN A:502 , ASN B:349 , GLY B:371 , ASN B:372 , ASP B:394 , CL B:505binding site for residue CL B 507
15AD6SOFTWAREGLU A:392 , ZN A:501 , SO4 A:506 , HIS B:303binding site for residue CL B 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U09)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4U09)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U09)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U09)

(-) Exons   (0, 0)

(no "Exon" information available for 4U09)

(-) 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:392
                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh.eee.........hhhhhhh....eee....hhhhh..hhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee...........hhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee......hhhhhhhhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u09 A  26 IQKPYKNLAKALQNPADVRNLDLSFQGLKTLPNKIGQLKNLQKLDLGGNEPTILSKEIWQLKDLQKLNLNNNKLTVLPKEIGQLQNLQELSLHSNELVNLPKEIGQFKNLQKLNLDNNKLTVLPKEIGQLQNLQELSLLSNKLISLPTEIEQLKSLKNLDLNHNEFTTVSKEVmLLETLENLDLRSNKLKTIPKEIRQLKSLKVLmLTGNQLTSLPKEIEQLQNLKTLNLGENRFQIFPVEILELKNLLELNLYYNQLVEFPKEVGQLKSLKYLSLYHNQITTLPVEVTQLPDLQELHLSGNKITILPKEILQLKNLEWLSLSNNKLNALPKEIGQLKKLQRLELGNNQLTTLPKEIEQLKNLQRLELDSNPISPKEKERIRKLLPKCEIDF 417
                                    35        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  
                                                                                                                                                                                                       199-MSE                         231-MSE                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:396
                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh.eee.........hhhhhhh....eee....hhhhh..hhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhh.....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee......hhhhhhhhhhhh...eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4u09 B  26 IQKPYKNLAKALQNPADVRNLDLSFQGLKTLPNKIGQLKNLQKLDLGGNEPTILSKEIWQLKDLQKLNLNNNKLTVLPKEIGQLQNLQELSLHSNELVNLPKEIGQFKNLQKLNLDNNKLTVLPKEIGQLQNLQELSLLSNKLISLPTEIEQLKSLKNLDLNHNEFTTVSKEVmLLETLENLDLRSNKLKTIPKEIRQLKSLKVLmLTGNQLTSLPKEIEQLQNLKTLNLGENRFQIFPVEILELKNLLELNLYYNQLVEFPKEVGQLKSLKYLSLYHNQITTLPVEVTQLPDLQELHLSGNKITILPKEILQLKNLEWLSLSNNKLNALPKEIGQLKKLQRLELGNNQLTTLPKEIEQLKNLQRLELDSNPISPKEKERIRKLLPKCEIDFEGGG 421
                                    35        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      
                                                                                                                                                                                                       199-MSE                         231-MSE
   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 4U09)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U09)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U09)

(-) Gene Ontology  (1, 1)

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4tzh 4u06 4u08