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(-) Description

Title :  CRYSTAL STRUCTURE OF STABILIZED TEM-1 BETA-LACTAMASE VARIANT V.13
 
Authors :  E. Dellus-Gur, A. Toth-Petroczy, M. Elias, D. S. Tawfik
Date :  09 Dec 12  (Deposition) - 03 Apr 13  (Release) - 17 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.68
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Keywords :  Tem-1 Beta-Lactamase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Dellus-Gur, A. Toth-Petroczy, M. Elias, D. S. Tawfik
What Makes A Protein Fold Amenable To Functional Innovation Fold Polarity And Stability Trade-Offs.
J. Mol. Biol. V. 425 2609 2013
PubMed-ID: 23542341  |  Reference-DOI: 10.1016/J.JMB.2013.03.033

(-) Compounds

Molecule 1 - BETA-LACTAMASE TEM
    ChainsA, B, C, D, E
    EC Number3.5.2.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneBLA, BLAT-3, BLAT-4, BLAT-5, BLAT-6
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymIRT-4, PENICILLINASE, TEM-1, TEM-16/CAZ-7, TEM-2, TEM- 24/CAZ-6, TEM-3, TEM-4, TEM-5, TEM-6, TEM-8/CAZ-2

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit ABCDE
Biological Unit 1 (1x)A    
Biological Unit 2 (1x) B   
Biological Unit 3 (1x)  C  
Biological Unit 4 (1x)   D 
Biological Unit 5 (1x)    E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MES3Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MES-1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3SO41Ligand/IonSULFATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3SO4-1Ligand/IonSULFATE ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MES-1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3SO4-1Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:37 , ASP A:38 , HOH A:425 , GLU B:37 , ASP B:38 , HOH B:412 , HOH B:415 , HOH B:420BINDING SITE FOR RESIDUE CA A 301
2AC2SOFTWARESER A:130 , VAL A:216 , LYS A:234 , SER A:235 , GLY A:236 , ALA A:237 , ARG A:244BINDING SITE FOR RESIDUE MES A 302
3AC3SOFTWARETYR B:105 , VAL B:216 , SER B:235 , GLY B:236 , ALA B:237 , ARG B:244BINDING SITE FOR RESIDUE MES B 301
4AC4SOFTWAREGLU C:37 , ASP C:38 , HOH C:407 , GLU E:37 , ASP E:38 , HOH E:306BINDING SITE FOR RESIDUE CA C 301
5AC5SOFTWARESER C:130 , VAL C:216 , SER C:235 , GLY C:236 , ALA C:237 , ARG C:244 , HOH C:411BINDING SITE FOR RESIDUE SO4 C 302
6AC6SOFTWARETYR D:105 , SER D:130 , VAL D:216 , SER D:235 , GLY D:236 , ALA D:237 , ARG D:244 , HOH D:409BINDING SITE FOR RESIDUE MES D 301

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1A:77 -A:123
2B:77 -B:123
3C:77 -C:123
4D:77 -D:123
5E:77 -E:123

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Glu A:166 -Pro A:167
2Glu B:166 -Pro B:167
3Glu C:166 -Pro C:167
4Glu D:166 -Pro D:167
5Glu E:166 -Pro E:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IBX)

(-) 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:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains d4ibxa_ A: beta-Lactamase, class A                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.eeeeeeee.....eeeee.....ee.hhhhhhhhhhhhhhhhhh.......ee.....................eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ibx A  26 HPETLVKVKDAEDQLGGRVGYIELDLASGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVGELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPVAMATTLRKLLTGELLTAASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW 290
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246     ||257       267       277       287   
                                                                                                                                                                                                                                              238|         252|                                    
                                                                                                                                                                                                                                               240          254                                    

Chain B from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains d4ibxb_ B: beta-Lactamase, class A                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.eeeeeeee.....eeeee.....ee.hhhhhhhhhhhhhhhhhh.......ee............hhhhh....eehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ibx B  26 HPETLVKVKDAEDQLGGRVGYIELDLASGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVGELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPVAMATTLRKLLTGELLTAASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW 290
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246     ||257       267       277       287   
                                                                                                                                                                                                                                              238|         252|                                    
                                                                                                                                                                                                                                               240          254                                    

Chain C from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains d4ibxc_ C: beta-Lactamase, class A                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.eeeeeeee.....eeeee.....ee...hhhhhhhhhhhhhhhh.......ee..hhhhh.....hhhhh....eehhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhh.....eeeeeeeee...eeeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ibx C  26 HPETLVKVKDAEDQLGGRVGYIELDLASGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVGELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPVAMATTLRKLLTGELLTAASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW 290
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246     ||257       267       277       287   
                                                                                                                                                                                                                                              238|         252|                                    
                                                                                                                                                                                                                                               240          254                                    

Chain D from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains d4ibxd_ D: beta-Lactamase, class A                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..eeeeeeee.....eeeee.....ee...hhhhhhhhhhhhhhhh.......ee..hhhhh.....hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ibx D  26 HPETLVKVKDAEDQLGGRVGYIELDLASGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVGELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPVAMATTLRKLLTGELLTAASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW 290
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246     ||257       267       277       287   
                                                                                                                                                                                                                                              238|         252|                                    
                                                                                                                                                                                                                                               240          254                                    

Chain E from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains d4ibxe_ E: beta-Lactamase, class A                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.eeeeeeee.....eeeee.....ee...hhhhhhhhhhhhhhhh.......ee.....................eehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.............hhhhh........eehhhhhhhhhhhh......hhhhhhhhhhhhhh................eeeeeeee.....eeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ibx E  26 HPETLVKVKDAEDQLGGRVGYIELDLASGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVGELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPVAMATTLRKLLTGELLTAASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW 290
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246     ||257       267       277       287   
                                                                                                                                                                                                                                              238|         252|                                    
                                                                                                                                                                                                                                               240          254                                    

   Legend:   → Mismatch (orange background)
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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, 5)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BLAT_ECOLX | P625931axb 1bt5 1btl 1ck3 1erm 1ero 1erq 1esu 1fqg 1jtd 1jtg 1jvj 1jwp 1jwv 1jwz 1lhy 1li0 1li9 1m40 1nxy 1ny0 1nym 1nyy 1pzo 1pzp 1s0w 1tem 1xpb 1xxm 1yt4 1zg4 1zg6 2b5r 2v1z 2v20 3c7u 3c7v 3cmz 3dtm 3jyi 3toi 4dxb 4dxc 4gku 4ibr 4id4 4mez 4qy5 4qy6 4r4r 4r4s 4rva 4rx2 4rx3 4zj1 4zj2 4zj3 5hvi 5hw1 5hw5 5i52 5i63 5iq8 5kkf

(-) Related Entries Specified in the PDB File

4ibr SAME STABILIZED TEM1 VARIANT CARRYING G238S/E104K MUTATIONS