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(-) Description

Title :  CRYSTAL STRUCTURE OF SERRATIA FONTICOLA CARBAPENEMASE SFC-1
 
Authors :  F. Fonseca, J. Spencer
Date :  18 Apr 12  (Deposition) - 23 May 12  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.38
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Beta-Lactamase, Carbapenemase, Hydrolase, Antibiotic Resistance (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Fonseca, E. I. Chudyk, M. W. Van Der Kamp, A. Correia, A. J. Mulholland, J. Spencer
The Basis For Carbapenem Hydrolysis By Class A Beta-Lactamases: A Combined Investigation Using Crystallography And Simulations.
J. Am. Chem. Soc. V. 134 18275 2012
PubMed-ID: 23030300  |  Reference-DOI: 10.1021/JA304460J

(-) Compounds

Molecule 1 - CARBAPENEM-HYDROLIZING BETA-LACTAMASE SFC-1
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26-B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 27-309
    Gene: BLASFC-1, SFC-1
    Organism Scientific: SERRATIA FONTICOLA
    Organism Taxid: 47917
    Strain: UTAD54

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 26)

Asymmetric Unit (2, 26)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2NA22Ligand/IonSODIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2NA-1Ligand/IonSODIUM ION
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2NA-1Ligand/IonSODIUM ION

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:70 , LYS A:73 , SER A:130 , HOH A:519 , HOH A:521 , HOH A:857BINDING SITE FOR RESIDUE EDO A 401
02AC2SOFTWAREHOH A:556 , HOH A:751 , HOH B:536BINDING SITE FOR RESIDUE NA A 402
03AC3SOFTWARETRP A:251 , PRO A:258 , HIS B:205 , HOH B:612BINDING SITE FOR RESIDUE NA A 403
04AC4SOFTWARESER A:84 , GLU A:203BINDING SITE FOR RESIDUE NA A 404
05AC5SOFTWAREPRO A:268 , HOH A:607 , HOH A:713BINDING SITE FOR RESIDUE NA A 405
06AC6SOFTWARESER A:82 , GLN A:85 , GLN A:86BINDING SITE FOR RESIDUE NA A 406
07AC7SOFTWAREGLN A:191 , LYS A:192 , HOH A:541 , HOH A:681 , HOH A:737BINDING SITE FOR RESIDUE NA A 407
08AC8SOFTWAREGLN A:27 , ASP A:31 , LYS A:34BINDING SITE FOR RESIDUE NA A 408
09AC9SOFTWAREARG A:43 , SER A:266 , HOH A:569 , HOH A:815BINDING SITE FOR RESIDUE NA A 409
10BC1SOFTWAREALA A:255BINDING SITE FOR RESIDUE NA A 410
11BC2SOFTWAREASP A:163BINDING SITE FOR RESIDUE NA A 411
12BC3SOFTWAREHOH A:720BINDING SITE FOR RESIDUE NA A 412
13BC4SOFTWAREGLY B:156 , ASN B:158 , ALA B:185 , GLU B:188 , HOH B:512 , HOH B:741BINDING SITE FOR RESIDUE EDO B 401
14BC5SOFTWAREGLY B:239 , VAL B:240 , ARG B:270 , ASN B:271 , LYS B:273 , HOH B:516 , HOH B:591BINDING SITE FOR RESIDUE EDO B 402
15BC6SOFTWARESER B:70 , LYS B:73 , SER B:130 , HOH B:511 , HOH B:527 , HOH B:830BINDING SITE FOR RESIDUE EDO B 403
16BC7SOFTWAREHIS A:205 , HOH A:706 , HOH A:805 , HIS B:205BINDING SITE FOR RESIDUE NA B 404
17BC8SOFTWARELYS A:212 , ASP B:209 , LYS B:212 , HOH B:610BINDING SITE FOR RESIDUE NA B 405
18BC9SOFTWAREARG B:96 , THR B:115BINDING SITE FOR RESIDUE NA B 406
19CC1SOFTWAREGLY B:41 , LYS B:267 , HOH B:544 , HOH B:735BINDING SITE FOR RESIDUE NA B 407
20CC2SOFTWAREHOH A:560 , THR B:202 , GLN B:206 , HOH B:658BINDING SITE FOR RESIDUE NA B 408
21CC3SOFTWAREASN B:63 , LYS B:184 , HOH B:782BINDING SITE FOR RESIDUE NA B 409
22CC4SOFTWAREHOH B:540BINDING SITE FOR RESIDUE NA B 410
23CC5SOFTWAREALA B:227 , TRP B:229 , HOH B:584BINDING SITE FOR RESIDUE NA B 411
24CC6SOFTWAREPRO B:107 , NA B:414 , HOH B:582 , HOH B:694BINDING SITE FOR RESIDUE NA B 412
25CC7SOFTWAREASP B:293 , HOH B:518 , HOH B:712BINDING SITE FOR RESIDUE NA B 413
26CC8SOFTWAREGLU B:110 , NA B:412 , HOH B:566BINDING SITE FOR RESIDUE NA B 414

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:69 -A:238
2B:69 -B:238

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:166 -Leu A:167
2Glu B:166 -Leu B:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EQI)

(-) 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:271
                                                                                                                                                                                                                                                                                                                
               SCOP domains d4eqia_ A: automated matches                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee...hhhhhhhhhhhhhhh...hhhh.ee..........hhhhhhh....eehhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhh...........hhhhhh.......eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeee......eeeeeeee......eeeeeeee........hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4eqi A   23 SQPPQVTVDKLKRLENDFGGRIGVYAIDTGSNKTFGYRANERFPLCSSFKGFLAAAVLSKSQQQEGLLNQRIRYDNRVMEPHSPVTEKQITTGMTVAELSAATLQYSDNGAANLLLEKLIGGPEGMTSFMRSIGDNVFRLDRWELELNSAIPGDDRDTSTPKAVAESMQKLAFGNVLGLTERHQLMDWFKGNTTGGARIRASVPANWVVGDKTGTCGVYGTANDYAVIWPVAHAPIVLAVYTSKPDRNSKHSDAVIADASRIVLESFNIDA  294
                                    32        42        52    ||  63        73        83        93       103       113       123       133       142       152       162       172       182       192       202       212       222       232       242       252|      263       273       283       293 
                                                             57|                                                                              140A                                                                                                             252|                                        
                                                              59                                                                                                                                                                                                254                                        


Chain B from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4eqib_ B: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee...hhhhhhhhhhhhhhh...hhhh.ee..........hhhhhhh....eehhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeee......eeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4eqi B   22 ASQPPQVTVDKLKRLENDFGGRIGVYAIDTGSNKTFGYRANERFPLCSSFKGFLAAAVLSKSQQQEGLLNQRIRYDNRVMEPHSPVTEKQITTGMTVAELSAATLQYSDNGAANLLLEKLIGGPEGMTSFMRSIGDNVFRLDRWELELNSAIPGDDRDTSTPKAVAESMQKLAFGNVLGLTERHQLMDWFKGNTTGGARIRASVPANWVVGDKTGTCGVYGTANDYAVIWPVAHAPIVLAVYTSKPDRNSKHSDAVIADASRIVLESFNIDALR  296
                                    31        41        51     || 62        72        82        92       102       112       122       132       141       151       161       171       181       191       201       211       221       231       241       251||     262       272       282       292    
                                                              57|                                                                              140A                                                                                                             252|                                          
                                                               59                                                                                                                                                                                                254
   Legend:   → Mismatch (orange background)
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    → 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  (1, 2)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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        Q6JP75_SERFO | Q6JP75: 4euz 4ev4

(-) Related Entries Specified in the PDB File

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