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(-) Description

Title :  LPXR FROM SALMONELLA TYPHIMURIUM
 
Authors :  L. Rutten, P. Gros
Date :  11 Dec 08  (Deposition) - 10 Feb 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lipopolysaccharide-Modifying Outer Membrane Enzyme, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Rutten, J. -P. B. A. Mannie, C. M. Stead, C. R. H. Raetz, C. M. Reynolds A. M. J. J. Bonvin, J. P. Tommassen, M. R. Egmond, M. S. Trent, P. Gros
Active-Site Architecture And Catalytic Mechanism Of The Lipid A Deacylase Lpxr Of Salmonella Typhimurium
Proc. Natl. Acad. Sci. Usa V. 106 1960 2009
PubMed-ID: 19174515  |  Reference-DOI: 10.1073/PNAS.0813064106

(-) Compounds

Molecule 1 - PUTATIVE OUTER MEMBRANE PROTEIN (LPXR)
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21STAR(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: MATURE DOMAIN, UNP RESIDUES 24-319
    Gene: LPXR
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602
    Strain: STRAIN LT2

 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  (3, 21)

Asymmetric Unit (3, 21)
No.NameCountTypeFull Name
1CXE8Ligand/IonPENTAETHYLENE GLYCOL MONODECYL ETHER
2GOL4Ligand/IonGLYCEROL
3ZN9Ligand/IonZINC ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CXE4Ligand/IonPENTAETHYLENE GLYCOL MONODECYL ETHER
2GOL2Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1CXE4Ligand/IonPENTAETHYLENE GLYCOL MONODECYL ETHER
2GOL2Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:1 , ASP A:44 , PHE A:296 , ZN A:298 , HOH A:475BINDING SITE FOR RESIDUE ZN A 297
02AC2SOFTWARESER A:1 , TYR A:41 , HIS A:43 , ZN A:297 , HOH B:431BINDING SITE FOR RESIDUE ZN A 298
03AC3SOFTWAREHIS A:54 , HIS A:84 , ASP A:104 , HOH A:338BINDING SITE FOR RESIDUE ZN A 299
04AC4SOFTWAREHIS A:25 , ASP A:29 , HIS B:25 , ASP B:29BINDING SITE FOR RESIDUE ZN A 300
05AC5SOFTWAREASN A:9 , ASP A:10 , THR A:34 , GOL A:303BINDING SITE FOR RESIDUE ZN A 301
06AC6SOFTWARETYR A:60 , ARG A:77 , PHE A:176 , ARG A:226 , ASN A:231 , THR A:233 , GLU A:278 , HOH A:412 , HOH A:466BINDING SITE FOR RESIDUE GOL A 302
07AC7SOFTWAREASN A:9 , ASP A:10 , THR A:34 , ZN A:301 , HOH A:331 , HOH A:376BINDING SITE FOR RESIDUE GOL A 303
08AC8SOFTWARESER A:18BINDING SITE FOR RESIDUE CXE A 304
09AC9SOFTWARESER A:18 , VAL A:219BINDING SITE FOR RESIDUE CXE A 305
10BC1SOFTWARELEU A:22 , TYR A:23 , GLY A:222 , TYR A:255BINDING SITE FOR RESIDUE CXE A 306
11BC2SOFTWARELEU A:151 , GLU A:167 , GLY A:182 , VAL A:223 , ARG A:225BINDING SITE FOR RESIDUE CXE A 307
12BC3SOFTWARESER B:1 , ASP B:44 , ZN B:298BINDING SITE FOR RESIDUE ZN B 297
13BC4SOFTWARESER B:1 , TYR B:41 , HIS B:43 , ZN B:297 , HOH B:431BINDING SITE FOR RESIDUE ZN B 298
14BC5SOFTWAREHIS B:54 , HIS B:84 , ASP B:104 , HOH B:327BINDING SITE FOR RESIDUE ZN B 299
15BC6SOFTWAREASN B:9 , ASP B:10 , THR B:34 , GOL B:302BINDING SITE FOR RESIDUE ZN B 300
16BC7SOFTWARETYR B:60 , ARG B:77 , LEU B:201 , ARG B:226 , ASN B:231 , THR B:233 , GLU B:278 , HOH B:416 , HOH B:426 , HOH B:493BINDING SITE FOR RESIDUE GOL B 301
17BC8SOFTWAREASN B:9 , ASP B:10 , THR B:34 , ZN B:300 , HOH B:482 , HOH B:553BINDING SITE FOR RESIDUE GOL B 302
18BC9SOFTWARESER B:18BINDING SITE FOR RESIDUE CXE B 303
19CC1SOFTWAREILE A:157 , SER B:18BINDING SITE FOR RESIDUE CXE B 304
20CC2SOFTWARELEU B:22 , LYS B:274BINDING SITE FOR RESIDUE CXE B 305
21CC3SOFTWAREPRO B:166 , GLU B:167 , VAL B:168 , GLY B:182 , VAL B:223 , ARG B:225 , ASP B:253BINDING SITE FOR RESIDUE CXE B 306

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:264 -Pro A:265
2Ser B:264 -Pro B:265

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FID)

(-) 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:296
 aligned with Q8ZPT3_SALTY | Q8ZPT3 from UniProtKB/TrEMBL  Length:319

    Alignment length:296
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313      
         Q8ZPT3_SALTY    24 SSLAISVANDDAGIFQPSLNALYGHPAADRGDYTAGLFLGYSHDLTDASQLSFHIAQDIYSPSGANKRKPEAVKGDRAFSAFLHTGLEWNSLATNWLRYRLGTDIGVIGPDAGGQEVQNRAHRIIGAEKYPAWQDQIENRYGYTAKGMVSLTPAIDILGVNVGFYPEVSAVGGNLFQYLGYGATVALGNDKTFNSDNGFGLLSRRGLIHTQKEGLIYKVFAGVERREVDKNYTLQGKTLQTKMETVDINKTVDEYRVGATIGYSPVAFSLSLNKVTSEFRTGDDYSYINGDITFFF 319
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fidA00 A:1-296 Putative outer membrane protein (lpxr)                                                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeeeeee....eeeeeeeeeeee..hhhhhhh..........eeeeeeeeeeeeeee..eeeeeeeeeeee.hhhhhhhhhhhhhhhhh...hhhhhhh...eeeeeeeeeeee..eeee..eeeeeeeeeeeeee..eeeeeeeeeeeee.hhhhhh...hhhhh...........eeeeeeeeeeeeeeeeehhhhh..............eeeeeeeeeeeee..eeeeeeeeee.........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fid A   1 SSLAISVANDDAGIFQPSLNALYGHPAADRGDYTAGLFLGYSHDLTDASQLSFHIAQDIYSPSGANKRKPEAVKGDRAFSAFLHTGLEWNSLATNWLRYRLGTDIGVIGPDAGGQEVQNRAHRIIGAEKYPAWQDQIENRYGYTAKGMVSLTPAIDILGVNVGFYPEVSAVGGNLFQYLGYGATVALGNDKTFNSDNGFGLLSRRGLIHTQKEGLIYKVFAGVERREVDKNYTLQGKTLQTKMETVDINKTVDEYRVGATIGYSPVAFSLSLNKVTSEFRTGDDYSYINGDITFFF 296
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290      


Chain B from PDB  Type:PROTEIN  Length:296
 aligned with Q8ZPT3_SALTY | Q8ZPT3 from UniProtKB/TrEMBL  Length:319

    Alignment length:296
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313      
         Q8ZPT3_SALTY    24 SSLAISVANDDAGIFQPSLNALYGHPAADRGDYTAGLFLGYSHDLTDASQLSFHIAQDIYSPSGANKRKPEAVKGDRAFSAFLHTGLEWNSLATNWLRYRLGTDIGVIGPDAGGQEVQNRAHRIIGAEKYPAWQDQIENRYGYTAKGMVSLTPAIDILGVNVGFYPEVSAVGGNLFQYLGYGATVALGNDKTFNSDNGFGLLSRRGLIHTQKEGLIYKVFAGVERREVDKNYTLQGKTLQTKMETVDINKTVDEYRVGATIGYSPVAFSLSLNKVTSEFRTGDDYSYINGDITFFF 319
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fidB00 B:1-296 Putative outer membrane protein (lpxr)                                                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeee..hhhhhhh..........eeeeeeeeeeeeeee..eeeeeeeeeeee.hhhhhhhhhhhhhhhh....hhhhhhh...eeeeeeeeeeee..eeee..eeeeeeeeeeeeee..eeeeeeeeeeeee.hhhhhh...hhhhh...........eeeeeeeeeeeeeeeeehhhhh..............eeeeeeeeeeeee..eeeeeeeeee.........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fid B   1 SSLAISVANDDAGIFQPSLNALYGHPAADRGDYTAGLFLGYSHDLTDASQLSFHIAQDIYSPSGANKRKPEAVKGDRAFSAFLHTGLEWNSLATNWLRYRLGTDIGVIGPDAGGQEVQNRAHRIIGAEKYPAWQDQIENRYGYTAKGMVSLTPAIDILGVNVGFYPEVSAVGGNLFQYLGYGATVALGNDKTFNSDNGFGLLSRRGLIHTQKEGLIYKVFAGVERREVDKNYTLQGKTLQTKMETVDINKTVDEYRVGATIGYSPVAFSLSLNKVTSEFRTGDDYSYINGDITFFF 296
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   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 3FID)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8ZPT3_SALTY | Q8ZPT3)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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