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(-) Description

Title :  CRYSTAL STRUCTURE OF THE UBIQUITIN K11S MUTANT
 
Authors :  P. J. Loll, P. J. Xu, J. Schmidt, S. L. Melideo
Date :  08 May 14  (Deposition) - 29 Oct 14  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Entropy-Reduction, Mutant, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. J. Loll, P. Xu, J. T. Schmidt, S. L. Melideo
Enhancing Ubiquitin Crystallization Through Surface-Entropy Reduction.
Acta Crystallogr. , Sect. F V. 70 1434 2014
PubMed-ID: 25286958  |  Reference-DOI: 10.1107/S2053230X14019244

(-) Compounds

Molecule 1 - UBIQUITIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSETA
    Expression System Strain: ROSETTA2(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CL8Ligand/IonCHLORIDE ION
3NA1Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NA-1Ligand/IonSODIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NA-1Ligand/IonSODIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NA-1Ligand/IonSODIUM ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NA-1Ligand/IonSODIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:206 , HOH B:204 , HOH B:213 , THR D:12 , HOH D:207 , HOH D:215 , HOH D:224binding site for residue CA A 101
02AC2SOFTWARELEU A:71 , LEU C:71binding site for residue CL A 102
03AC3SOFTWARELEU A:15 , GLU A:16binding site for residue CL A 103
04AC4SOFTWAREASN B:60 , HOH B:212 , HOH B:217binding site for residue CA B 101
05AC5SOFTWARETYR B:59 , GLU D:18 , HOH D:222binding site for residue NA B 102
06AC6SOFTWARELEU C:15 , GLU C:16 , HOH C:245binding site for residue CL C 101
07AC7SOFTWAREHIS B:68 , GLN C:49 , HOH C:226binding site for residue CL C 102
08AC8SOFTWAREHIS C:68 , LYS D:6 , HIS D:68binding site for residue CL C 103
09AC9SOFTWAREGLU A:24 , HOH A:225 , HOH A:227 , ASP D:32 , HOH D:203binding site for residue CA D 101
10AD1SOFTWAREGLU D:24 , ASP D:52 , HOH D:256binding site for residue CA D 102
11AD2SOFTWARELEU B:71 , LEU D:71 , HOH D:227binding site for residue CL D 103
12AD3SOFTWARELEU D:15 , GLU D:16 , HOH D:235 , HOH D:244binding site for residue CL D 104
13AD4SOFTWAREARG D:42 , ARG D:72 , HOH D:229binding site for residue CL D 105

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PIG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PIG)

(-) 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:75
                                                                                                          
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                  4pig A  1 MQIFVKTLTGSTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG 75
                                    10        20        30        40        50        60        70     


Chain B from PDB  Type:PROTEIN  Length:76
                                                                                                           
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                  4pig B  1 MQIFVKTLTGSTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76
                                    10        20        30        40        50        60        70      


Chain C from PDB  Type:PROTEIN  Length:75
                                                                                                          
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                  4pig C  1 MQIFVKTLTGSTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG 75
                                    10        20        30        40        50        60        70     


Chain D from PDB  Type:PROTEIN  Length:76
                                                                                                           
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                  4pig D  1 MQIFVKTLTGSTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76
                                    10        20        30        40        50        60        70
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  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 4PIG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (92, 92)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RL40_HUMAN | P62987: 1c3t 1cmx 1d3z 1f9j 1fxt 1g6j 1gjz 1nbf 1q5w 1s1q 1sif 1tbe 1ubi 1ubq 1ud7 1uzx 1xd3 1yx5 1yx6 1zo6 2ayo 2bgf 2den 2fuh 2g45 2gbj 2gbk 2gbm 2gbn 2gbr 2hth 2ibi 2j7q 2jf5 2jzz 2k6d 2k8b 2k8c 2kdf 2khw 2kjh 2klg 2kn5 2kox 2ktf 2kwu 2kwv 2l0f 2l0t 2lj5 2mbh 2mjb 2mur 2n3u 2n3v 2n3w 2nbd 2nbe 2nr2 2o6v 2ojr 2pe9 2pea 2rsu 2w9n 2wdt 2xew 2xk5 2zcb 3a33 3by4 3c0r 3dvg 3dvn 3eec 3efu 3ehv 3h7p 3h7s 3hm3 3i3t 3ifw 3ihp 3jsv 3jvz 3jw0 3k9p 3kvf 3kw5 3ldz 3mhs 3mtn 3n30 3n32 3n3k 3nhe 3nob 3ns8 3phd 4hjk 4jio 4p4h 4pih 4pij 4rf0 4rf1 4s1z 4ug0 4v6x 4xkl 5aj0 5go7 5go8 5gob 5goc 5god 5gog 5goh 5goi 5goj 5gok 5hpk 5hpl 5hps 5hpt 5j26 5j8p 5jbv 5jby 5t2c

(-) Related Entries Specified in the PDB File

4pih 4pij