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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ARGININE 3RD TRANSPORT SYSTEM PERIPLASMIC BINDING PROTEIN FROM LEGIONELLA PNEUMOPHILA
 
Authors :  K. Palani, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  08 Dec 09  (Deposition) - 22 Dec 09  (Release) - 22 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Biol. Unit 4:  C  (1x)
Biol. Unit 5:  D  (1x)
Keywords :  Arginine Transport System, Periplasmic Binding Protein, Legionella Pneumophila, Protein Structure Initiative Ii(Psi Ii), Nysgxrc, 11316I, Structural Genomics, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Palani, S. K. Burley, S. Swaminathan
Crystal Structure Of An Arginine 3Rd Transport System Periplasmic Binding Protein From Legionella Pneumophila
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ARGININE 3RD TRANSPORT SYSTEM PERIPLASMIC BINDING PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 18-245
    Gene: ARTJ, LPG1555
    Organism Scientific: LEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA STR. PHILADELPHIA 1
    Organism Taxid: 272624
    Strain: STRAIN PHILADELPHIA 1/ATCC 33152/DSM 7513

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): A   
Biological Unit 3 (1x):  B  
Biological Unit 4 (1x):   C 
Biological Unit 5 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 32)

Asymmetric Unit (1, 32)
No.NameCountTypeFull Name
1MSE32Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 32)
No.NameCountTypeFull Name
1MSE32Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 5 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3KZG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Pro A:30 -Pro A:31
2Glu A:185 -Pro A:186
3Pro B:30 -Pro B:31
4Glu B:185 -Pro B:186
5Pro C:30 -Pro C:31
6Glu C:185 -Pro C:186
7Pro D:30 -Pro D:31
8Glu D:185 -Pro D:186

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KZG)

(-) 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:228
 aligned with Q5ZV85_LEGPH | Q5ZV85 from UniProtKB/TrEMBL  Length:245

    Alignment length:228
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237        
         Q5ZV85_LEGPH    18 SLNLTIGTSKFNPPFEVWSGNNSSLYGFDIDLMQEICRRLHATCTFEAYIFDDLFPALKNREVDLVIASMIITDERKKHFIFSLPYMESNSQYITTVDSKISTFDDLHGKKIGVRKGTPYARQVLSENRNNQVIFYELIQDMLLGLSNNQVDASLMDYEAAKYWMASEPYAYKLIGKKYKLIGKKISIGEGYSIMANPDQFVLIKKINKILLEMEADGTYLRLYSEYF 245
               SCOP domains d3kzga_ A: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee.ee...ee.........hhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhh....ee........hhhhh.ee.......eeeeeee......hhhhhh..eeeee...hhhhhhhhh....eeeee.hhhhhhhhhhh....eeeeehhhhhhhhh....hhhhhh..eeeeeeeee.......eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kzg A  18 SLNLTIGTSKFNPPFEVWSGNNSSLYGFDIDLmQEICRRLHATCTFEAYIFDDLFPALKNREVDLVIASmIITDERKKHFIFSLPYmESNSQYITTVDSKISTFDDLHGKKIGVRKGTPYARQVLSENRNNQVIFYELIQDmLLGLSNNQVDASLmDYEAAKYWmASEPYAYKLIGKKYKLIGKKISIGEGYSImANPDQFVLIKKINKILLEmEADGTYLRLYSEYF 245
                                    27        37        47  |     57        67        77        87        97      |107       117       127       137       147       157 |     167     | 177    |  187       197       207    |  217       227   |   237        
                                                           50-MSE                               87-MSE          104-MSE                                                159-MSE       173-MSE  182-MSE                       212-MSE            231-MSE          


Chain B from PDB  Type:PROTEIN  Length:228
 aligned with Q5ZV85_LEGPH | Q5ZV85 from UniProtKB/TrEMBL  Length:245

    Alignment length:228
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237        
         Q5ZV85_LEGPH    18 SLNLTIGTSKFNPPFEVWSGNNSSLYGFDIDLMQEICRRLHATCTFEAYIFDDLFPALKNREVDLVIASMIITDERKKHFIFSLPYMESNSQYITTVDSKISTFDDLHGKKIGVRKGTPYARQVLSENRNNQVIFYELIQDMLLGLSNNQVDASLMDYEAAKYWMASEPYAYKLIGKKYKLIGKKISIGEGYSIMANPDQFVLIKKINKILLEMEADGTYLRLYSEYF 245
               SCOP domains d3kzgb_ B: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee.ee...eee......eehhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhh....ee......hhhhhh..ee.......eeeeeee......hhhhhh..eeeee...hhhhhhhhh....eeeee.hhhhhhhhhhh....eeeeehhhhhhh..............eeeeeeeee.......eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kzg B  18 SLNLTIGTSKFNPPFEVWSGNNSSLYGFDIDLmQEICRRLHATCTFEAYIFDDLFPALKNREVDLVIASmIITDERKKHFIFSLPYmESNSQYITTVDSKISTFDDLHGKKIGVRKGTPYARQVLSENRNNQVIFYELIQDmLLGLSNNQVDASLmDYEAAKYWmASEPYAYKLIGKKYKLIGKKISIGEGYSImANPDQFVLIKKINKILLEmEADGTYLRLYSEYF 245
                                    27        37        47  |     57        67        77        87        97      |107       117       127       137       147       157 |     167     | 177    |  187       197       207    |  217       227   |   237        
                                                           50-MSE                               87-MSE          104-MSE                                                159-MSE       173-MSE  182-MSE                       212-MSE            231-MSE          


Chain C from PDB  Type:PROTEIN  Length:228
 aligned with Q5ZV85_LEGPH | Q5ZV85 from UniProtKB/TrEMBL  Length:245

    Alignment length:228
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237        
         Q5ZV85_LEGPH    18 SLNLTIGTSKFNPPFEVWSGNNSSLYGFDIDLMQEICRRLHATCTFEAYIFDDLFPALKNREVDLVIASMIITDERKKHFIFSLPYMESNSQYITTVDSKISTFDDLHGKKIGVRKGTPYARQVLSENRNNQVIFYELIQDMLLGLSNNQVDASLMDYEAAKYWMASEPYAYKLIGKKYKLIGKKISIGEGYSIMANPDQFVLIKKINKILLEMEADGTYLRLYSEYF 245
               SCOP domains d3kzgc_ C: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee.ee...eee......eehhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhh....ee......hhhhhh..ee.......eeeeeee......hhhhh...eeeee...hhhhhhhhh....eeeee.hhhhhhhhhhh....eeeeehhhhhhhhh............eeeeeeeee.......eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kzg C  18 SLNLTIGTSKFNPPFEVWSGNNSSLYGFDIDLmQEICRRLHATCTFEAYIFDDLFPALKNREVDLVIASmIITDERKKHFIFSLPYmESNSQYITTVDSKISTFDDLHGKKIGVRKGTPYARQVLSENRNNQVIFYELIQDmLLGLSNNQVDASLmDYEAAKYWmASEPYAYKLIGKKYKLIGKKISIGEGYSImANPDQFVLIKKINKILLEmEADGTYLRLYSEYF 245
                                    27        37        47  |     57        67        77        87        97      |107       117       127       137       147       157 |     167     | 177    |  187       197       207    |  217       227   |   237        
                                                           50-MSE                               87-MSE          104-MSE                                                159-MSE       173-MSE  182-MSE                       212-MSE            231-MSE          


Chain D from PDB  Type:PROTEIN  Length:228
 aligned with Q5ZV85_LEGPH | Q5ZV85 from UniProtKB/TrEMBL  Length:245

    Alignment length:228
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237        
         Q5ZV85_LEGPH    18 SLNLTIGTSKFNPPFEVWSGNNSSLYGFDIDLMQEICRRLHATCTFEAYIFDDLFPALKNREVDLVIASMIITDERKKHFIFSLPYMESNSQYITTVDSKISTFDDLHGKKIGVRKGTPYARQVLSENRNNQVIFYELIQDMLLGLSNNQVDASLMDYEAAKYWMASEPYAYKLIGKKYKLIGKKISIGEGYSIMANPDQFVLIKKINKILLEMEADGTYLRLYSEYF 245
               SCOP domains d3kzgd_ D: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---SBP_bac_3-3kzgD01 D:21-245                                                                                                                                                                                                        Pfam domains (1)
           Pfam domains (2) ---SBP_bac_3-3kzgD02 D:21-245                                                                                                                                                                                                        Pfam domains (2)
           Pfam domains (3) ---SBP_bac_3-3kzgD03 D:21-245                                                                                                                                                                                                        Pfam domains (3)
           Pfam domains (4) ---SBP_bac_3-3kzgD04 D:21-245                                                                                                                                                                                                        Pfam domains (4)
         Sec.struct. author ...eeeeee.ee...eee......eehhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhh....eeeeeee.hhhhhh..ee.......eeeeeee......hhhhh...eeeee...hhhhhhhhh....eeeee.hhhhhhhh.......eeeeehhhhhhhhhh...........eeeeeeeee....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kzg D  18 SLNLTIGTSKFNPPFEVWSGNNSSLYGFDIDLmQEICRRLHATCTFEAYIFDDLFPALKNREVDLVIASmIITDERKKHFIFSLPYmESNSQYITTVDSKISTFDDLHGKKIGVRKGTPYARQVLSENRNNQVIFYELIQDmLLGLSNNQVDASLmDYEAAKYWmASEPYAYKLIGKKYKLIGKKISIGEGYSImANPDQFVLIKKINKILLEmEADGTYLRLYSEYF 245
                                    27        37        47  |     57        67        77        87        97      |107       117       127       137       147       157 |     167     | 177    |  187       197       207    |  217       227   |   237        
                                                           50-MSE                               87-MSE          104-MSE                                                159-MSE       173-MSE  182-MSE                       212-MSE            231-MSE
   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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