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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI SBCD AT 2.5 ANGSTROM RESOLUTION
 
Authors :  S. Liu, L. F. Tian, X. X. Yan, D. C. Liang
Date :  25 Jul 13  (Deposition) - 27 Aug 14  (Release) - 27 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Meiotic Recombination 11 Homolog, Double-Strand Break Repair Protein, Nuclease , Endonuclease , Exonuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Liu, L. F. Tian, Y. P. Liu, X. M. An, Q. Tang, X. X. Yan, D. C. Liang
Structural Basis For Dna Recognition And Nuclease Processin By The Mre11 Homologue Sbcd In Double-Strand Breaks Repair.
Acta Crystallogr. , Sect. D V. 70 299 2014
PubMed-ID: 24531464  |  Reference-DOI: 10.1107/S139900471302693X

(-) Compounds

Molecule 1 - EXONUCLEASE SUBUNIT SBCD
    Chains: C, B, A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-340
    Gene: SBCD, EKO11_3451, KO11_21615
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 595495
    Strain: ATCC 55124 / KO11
    Synonym: NUCLEASE SBCCD, D SUBUNIT

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG C:60 , ASN C:64 , THR C:89 , LEU C:90 , GLU C:92 , SER C:93 , HOH C:632BINDING SITE FOR RESIDUE GOL C 401
2AC2SOFTWAREARG B:60 , ASN B:64 , THR B:89 , GLU B:92 , SER B:93 , GLU D:92 , HOH D:621BINDING SITE FOR RESIDUE GOL B 401
3AC3SOFTWAREARG A:60 , ASN A:64 , THR A:89 , SER A:93 , HOH A:630 , HOH C:632BINDING SITE FOR RESIDUE GOL A 401
4AC4SOFTWAREARG D:60 , TYR D:63 , ASN D:64 , THR D:89 , LEU D:90 , GLU D:92 , SER D:93 , HOH D:621BINDING SITE FOR RESIDUE GOL D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LU9)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gly B:146 -Ile B:147
2Glu B:302 -Pro B:303
3Val A:299 -Ser A:300
4Glu A:302 -Pro A:303
5Thr D:139 -Ser D:140
6Ala D:142 -Gly D:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LU9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LU9)

(-) Exons   (0, 0)

(no "Exon" information available for 4LU9)

(-) 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:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.............hhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh.eeee.......eeee.....eeeeee.....hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......................hhhhh....eeeee.....eee..eeeeee.......hhhhh....eeeeeeee..eeeeeeeee......eeeeeehhhhhhhhhhhhh.......eeeeeee....hhhhhhhhhhhhhh...eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lu9 A  -3 DIEFMRILHTSDWHLGQNFYSKSREAEHQAFLDWLLETAQTHQVDAIIVAGDVFDTGSPPSYARTLYNRFVVNLQQTGCHLVVLAGNHDSVATLNESRDIMAFLNTTVVASAGHAPQILPRRDGTPGAVLCPIPFLRPRDIITSQAGLNGIEKQQHLLAAITDYYQQHYADACKLRGDQPLPIIATGHLTTVGASKSDAVRDIYIGTLDAFPAQNFPPADYIALGHIHRAQIIGGMEHVRYCGSPIPLSFDECGKSKYVHLVTFSNGKLESVENLNVPVTQPMAVLKGDLASITAQLEQWRDVSQEPPVWLDIEITTDEYLHDIQRKIQALTESLPVEVLLVR 339
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336   


Chain B from PDB  Type:PROTEIN  Length:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.............hhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhh...eeee.......eeee.....eeeeee.....hhhhhh.............hhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......................hhhhh....eeeee.....eee..eeeeee.......hhhhh....eeeeeeee..eeeeeeeee......eeeeeehhhhhhhhhhhhh.......eeeeeee........hhhhhhhhh....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lu9 B  -1 EFMRILHTSDWHLGQNFYSKSREAEHQAFLDWLLETAQTHQVDAIIVAGDVFDTGSPPSYARTLYNRFVVNLQQTGCHLVVLAGNHDSVATLNESRDIMAFLNTTVVASAGHAPQILPRRDGTPGAVLCPIPFLRPRDIITSQAGLNGIEKQQHLLAAITDYYQQHYADACKLRGDQPLPIIATGHLTTVGASKSDAVRDIYIGTLDAFPAQNFPPADYIALGHIHRAQIIGGMEHVRYCGSPIPLSFDECGKSKYVHLVTFSNGKLESVENLNVPVTQPMAVLKGDLASITAQLEQWRDVSQEPPVWLDIEITTDEYLHDIQRKIQALTESLPVEVLLVRR 340
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338  


Chain C from PDB  Type:PROTEIN  Length:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee.......ee..eehhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhh..eeee.......eeee.....eeeeee.....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......................hhhhh....eeeee.....eee..eeeeee.......hhhhh....eeeeeeee..eeeeeeeee......eeee..hhhhhhhhhh....eeeee.......hhhhhhhhhhhhh...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lu9 C  -2 IEFMRILHTSDWHLGQNFYSKSREAEHQAFLDWLLETAQTHQVDAIIVAGDVFDTGSPPSYARTLYNRFVVNLQQTGCHLVVLAGNHDSVATLNESRDIMAFLNTTVVASAGHAPQILPRRDGTPGAVLCPIPFLRPRDIITSQAGLNGIEKQQHLLAAITDYYQQHYADACKLRGDQPLPIIATGHLTTVGASKSDAVRDIYIGTLDAFPAQNFPPADYIALGHIHRAQIIGGMEHVRYCGSPIPLSFDECGKSKYVHLVTFSNGKLESVENLNVPVTQPMAVLKGDLASITAQLEQWPPVWLDIEITTDEYLHDIQRKIQALTESLPVEVLLVR 339
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       303       313       323       333      
                                                                                                                                                                                                                                                                                                                                    296|                                    
                                                                                                                                                                                                                                                                                                                                     303                                    


Chain D from PDB  Type:PROTEIN  Length:344
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.............hhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhh...eeee.......eeee.....eeeeee.....hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......................hhhhh....eeeee.....eee..eeeeee.......hhhhh....eeeeeeee..eeeeeeeee......eeeeeehhhhhhhhhhhhh.......eeeeeee....hhhhhhhhhhhhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lu9 D  -3 DIEFMRILHTSDWHLGQNFYSKSREAEHQAFLDWLLETAQTHQVDAIIVAGDVFDTGSPPSYARTLYNRFVVNLQQTGCHLVVLAGNHDSVATLNESRDIMAFLNTTVVASAGHAPQILPRRDGTPGAVLCPIPFLRPRDIITSQAGLNGIEKQQHLLAAITDYYQQHYADACKLRGDQPLPIIATGHLTTVGASKSDAVRDIYIGTLDAFPAQNFPPADYIALGHIHRAQIIGGMEHVRYCGSPIPLSFDECGKSKYVHLVTFSNGKLESVENLNVPVTQPMAVLKGDLASITAQLEQWRDVSQEPPVWLDIEITTDEYLHDIQRKIQALTESLPVEVLLVRR 340
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336
   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 4LU9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LU9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LU9)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala D:142 - Gly D:143   [ RasMol ]  
    Glu A:302 - Pro A:303   [ RasMol ]  
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    Gly B:146 - Ile B:147   [ RasMol ]  
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 Related Entries

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(-) Related Entries Specified in the PDB File

4lty