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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI SBCD AT 1.8 A RESOLUTION
 
Authors :  S. Liu, L. F. Tian, X. X. Yan, D. C. Liang
Date :  24 Jul 13  (Deposition) - 26 Feb 14  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
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 15-354
    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 , SER C:93 , HOH C:515 , HOH C:541 , HOH C:599BINDING SITE FOR RESIDUE GOL C 401
2AC2SOFTWAREARG B:60 , TYR B:63 , ASN B:64 , THR B:89 , LEU B:90 , GLU B:92 , SER B:93 , HOH B:523 , HOH B:531BINDING SITE FOR RESIDUE GOL B 401
3AC3SOFTWAREARG A:60 , ASN A:64 , THR A:89 , LEU A:90 , GLU A:92 , SER A:93 , HOH A:562 , HOH A:721BINDING SITE FOR RESIDUE GOL A 401
4AC4SOFTWAREHOH B:556 , ARG D:60 , ASN D:64 , THR D:89 , LEU D:90 , GLU D:92 , SER D:93BINDING SITE FOR RESIDUE GOL D 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu B:302 -Pro B:303
2Thr A:139 -Ser A:140
3Glu A:302 -Pro A:303
4Arg D:297 -Asp D:298

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LTY)

(-) 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:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.......ee..eehhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhh...eeee.......eeee.....eeeeee.....hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......................hhhhh....eeeee.....eee..eeeeee.......hhhhh....eeeeeeee..eeeeeeeee......eeeeeehhhhhhhhhhhhh.......eeeeeee....hhhhhhhhhhhhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lty A  -4 MDIEFMRILHTSDWHLGQNFYSKSREAEHQAFLDWLLETAQTHQVDAIIVAGDVFDTGSPPSYARTLYNRFVVNLQQTGCHLVVLAGNHDSVATLNESRDIMAFLNTTVVASAGHAPQILPRRDGTPGAVLCPIPFLRPRDIITSQAGLNGIEKQQHLLAAITDYYQQHYADACKLRGDQPLPIIATGHLTTVGASKSDAVRDIYIGTLDAFPAQNFPPADYIALGHIHRAQIIGGMEHVRYCGSPIPLSFDECGKSKYVHLVTFSNGKLESVENLNVPVTQPMAVLKGDLASITAQLEQWRDVSQEPPVWLDIEITTDEYLHDIQRKIQALTESLPVEVLLVRR 340
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335     


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.hhhhh.......hhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......................hhhhh....eeeee.....eee..eeeeee.......hhhhh....eeeeeeee..eeeeeeeee......eeeeeeehhhhhhhhhhhh.......eeeeeeee...hhhhhhhhhhhhh....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lty 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:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......ee..eehhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhh...eeee.......eeee.....eeeeee.....hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......................hhhhh....eeeee.....eee..eeeeee.......hhhhh....eeeeeeee..eeeeeeeee......eeeee.hhhhhhhhh.......eeeee...hhhhhhhhhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lty C  -2 IEFMRILHTSDWHLGQNFYSKSREAEHQAFLDWLLETAQTHQVDAIIVAGDVFDTGSPPSYARTLYNRFVVNLQQTGCHLVVLAGNHDSVATLNESRDIMAFLNTTVVASAGHAPQILPRRDGTPGAVLCPIPFLRPRDIITSQEKQQHLLAAITDYYQQHYADACKLRGDQPLPIIATGHLTTVGASKSDAVRDIYIGTLDAFPAQNFPPADYIALGHIHRAQIIGGMEHVRYCGSPIPLSFDECGKSKYVHLVTFSNGKLESVENLNVPVTQPMAVLKGDLASITAQLEQQEPPVWLDIEIDEYLHDIQRKIQALTESLPVEVLLV 338
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137   ||  153       163       173       183       193       203       213       223       233       243       253       263       273       283       293 ||    308  ||   320       330        
                                                                                                                                                                         141|                                                                                                                                                295|       311|                        
                                                                                                                                                                          148                                                                                                                                                 301        314                        


Chain D from PDB  Type:PROTEIN  Length:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.......ee..eehhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhh...eeee.......eeee.....eeeeee.....hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......................hhhhh....eeeee.....eee..eeeeee.......hhhhh....eeeeeeee..eeeeeeeee......eeeeeehhhhhhhhhhhhh.......eeeeeee.....hhhhhhhhhhhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lty D  -4 MDIEFMRILHTSDWHLGQNFYSKSREAEHQAFLDWLLETAQTHQVDAIIVAGDVFDTGSPPSYARTLYNRFVVNLQQTGCHLVVLAGNHDSVATLNESRDIMAFLNTTVVASAGHAPQILPRRDGTPGAVLCPIPFLRPRDIITSQAGLNGIEKQQHLLAAITDYYQQHYADACKLRGDQPLPIIATGHLTTVGASKSDAVRDIYIGTLDAFPAQNFPPADYIALGHIHRAQIIGGMEHVRYCGSPIPLSFDECGKSKYVHLVTFSNGKLESVENLNVPVTQPMAVLKGDLASITAQLEQWRDVSQEPPVWLDIEITTDEYLHDIQRKIQALTESLPVEVLLVRR 340
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335
   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  (0, 0)

(no "SCOP Domain" information available for 4LTY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

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  4lty
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4lu9