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PDBsum entry 1jml
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protein metals links
Protein binding PDB id
1jml

 

 

 

 

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Contents
Protein chain
72 a.a. *
Metals
_ZN ×3
Waters ×39
* Residue conservation analysis
PDB id:
1jml
Name: Protein binding
Title: Conversion of monomeric protein l to an obligate dimer by computational protein design
Structure: Protein l. Chain: a. Fragment: b1 domain. Synonym: ig light chain-binding protein. Engineered: yes. Mutation: yes
Source: Finegoldia magna. Organism_taxid: 334413. Strain: atcc 29328. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
1.90Å     R-factor:   0.193     R-free:   0.218
Authors: J.W.O'Neill,B.Kuhlman,D.E.Kim,K.Y.J.Zhang,D.Baker
Key ref:
B.Kuhlman et al. (2001). Conversion of monomeric protein L to an obligate dimer by computational protein design. Proc Natl Acad Sci U S A, 98, 10687-10691. PubMed id: 11526208 DOI: 10.1073/pnas.181354398
Date:
19-Jul-01     Release date:   10-Oct-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q51912  (Q51912_FINMA) -  Gram-positive cocci surface proteins LPxTG domain-containing protein from Finegoldia magna
Seq:
Struc: 		 
Seq:
Struc: 		719 a.a.
72 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 13 residue positions (black crosses)

 

 
DOI no: 10.1073/pnas.181354398 Proc Natl Acad Sci U S A 98:10687-10691 (2001)
PubMed id: 11526208  
 
 
Conversion of monomeric protein L to an obligate dimer by computational protein design.
B.Kuhlman, J.W.O'Neill, D.E.Kim, K.Y.Zhang, D.Baker.
 
  ABSTRACT  
 
Protein L consists of a single alpha-helix packed on a four-stranded beta-sheet formed by two symmetrically opposed beta-hairpins. We use a computer-based protein design procedure to stabilize a domain-swapped dimer of protein L in which the second beta-turn straightens and the C-terminal strand inserts into the beta-sheet of the partner. The designed obligate dimer contains three mutations (A52V, N53P, and G55A) and has a dissociation constant of approximately 700 pM, which is comparable to the dissociation constant of many naturally occurring protein dimers. The structure of the dimer has been determined by x-ray crystallography and is close to the in silico model.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Simulated annealing composite omit map (2F[obs] F[calc]) of the VPA hinge region. The mutated residues (V52, P53, and A55) are highlighted in yellow. The electron density was contoured at 1 . 		Figure 5.
Fig. 5. Comparison of the VPA design model to the VPA crystal structure. (A) Shown in blue (asymmetric unit) and cyan (symmetry mate) are the two halves that constitute the VPA crystal structure, and in dark and light orange is the modeled VPA (based on the G55A structure). The overall main-chain rms deviation is 0.40 Å for the blue and orange structures. (B) A close-up of the mutated region.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20544969 L.Dai, Y.Yang, H.R.Kim, and Y.Zhou (2010).
Improving computational protein design by using structure-derived sequence profile.
  Proteins, 78, 2338-2348.  
20377257 R.J.Radford, P.C.Nguyen, T.B.Ditri, J.S.Figueroa, and F.A.Tezcan (2010).
Controlled protein dimerization through hybrid coordination motifs.
  Inorg Chem, 49, 4362-4369.
PDB code: 3l1m
19626705 J.L.Jordan, J.W.Arndt, K.Hanf, G.Li, J.Hall, S.Demarest, F.Huang, X.Wu, B.Miller, S.Glaser, E.J.Fernandez, D.Wang, and A.Lugovskoy (2009).
Structural understanding of stabilization patterns in engineered bispecific Ig-like antibody molecules.
  Proteins, 77, 832-841.
PDB codes: 3hc0 3hc3 3hc4
19260676 J.S.Butler, D.M.Mitrea, G.Mitrousis, G.Cingolani, and S.N.Loh (2009).
Structural and thermodynamic analysis of a conformationally strained circular permutant of barnase.
  Biochemistry, 48, 3497-3507.
PDB code: 3da7
19299503 K.Sato, C.Li, I.Salard, A.J.Thompson, M.J.Banfield, and C.Dennison (2009).
Metal-binding loop length and not sequence dictates structure.
  Proc Natl Acad Sci U S A, 106, 5616-5621.
PDB codes: 3fs9 3fsa 3fsv 3fsw 3fsz 3ft0
19074157 L.A.Clark, P.A.Boriack-Sjodin, E.Day, J.Eldredge, C.Fitch, M.Jarpe, S.Miller, Y.Li, K.Simon, and H.W.van Vlijmen (2009).
An antibody loop replacement design feasibility study and a loop-swapped dimer structure.
  Protein Eng Des Sel, 22, 93.
PDB code: 3eot
19038264 T.A.Cutler, B.M.Mills, D.J.Lubin, L.T.Chong, and S.N.Loh (2009).
Effect of interdomain linker length on an antagonistic folding-unfolding equilibrium between two protein domains.
  J Mol Biol, 386, 854-868.  
17729291 M.D.Altman, E.A.Nalivaika, M.Prabu-Jeyabalan, C.A.Schiffer, and B.Tidor (2008).
Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease.
  Proteins, 70, 678-694.
PDB codes: 2nxd 2nxl 2nxm
17471459 A.B.Chowdry, K.A.Reynolds, M.S.Hanes, M.Voorhies, N.Pokala, and T.M.Handel (2007).
An object-oriented library for computational protein design.
  J Comput Chem, 28, 2378-2388.  
17327666 M.Carson, D.H.Johnson, H.McDonald, C.Brouillette, and L.J.Delucas (2007).
His-tag impact on structure.
  Acta Crystallogr D Biol Crystallogr, 63, 295-301.  
17971437 X.Hu, H.Wang, H.Ke, and B.Kuhlman (2007).
High-resolution design of a protein loop.
  Proc Natl Acad Sci U S A, 104, 17668-17673.
PDB codes: 2rb8 2rbl
16105176 S.De, O.Krishnadev, N.Srinivasan, and N.Rekha (2005).
Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.
  BMC Struct Biol, 5, 15.  
15096200 A.L.Watters, and D.Baker (2004).
Searching for folded proteins in vitro and in silico.
  Eur J Biochem, 271, 1615-1622.  
15102454 B.Kuhlman, and D.Baker (2004).
Exploring folding free energy landscapes using computational protein design.
  Curr Opin Struct Biol, 14, 89-95.  
15130477 M.A.Schumacher, M.Crum, and M.C.Miller (2004).
Crystal structures of apocalmodulin and an apocalmodulin/SK potassium channel gating domain complex.
  Structure, 12, 849-860.
PDB codes: 1qx5 1qx7
14691235 S.J.Demarest, S.Deechongkit, H.J.Dyson, R.M.Evans, and P.E.Wright (2004).
Packing, specificity, and mutability at the binding interface between the p160 coactivator and CREB-binding protein.
  Protein Sci, 13, 203-210.  
15189881 S.Kundu, and R.L.Jernigan (2004).
Molecular mechanism of domain swapping in proteins: an analysis of slower motions.
  Biophys J, 86, 3846-3854.  
12623012 F.Rousseau, J.W.Schymkowitz, and L.S.Itzhaki (2003).
The unfolding story of three-dimensional domain swapping.
  Structure, 11, 243-251.  
12070322 A.Linhananta, H.Zhou, and Y.Zhou (2002).
The dual role of a loop with low loop contact distance in folding and domain swapping.
  Protein Sci, 11, 1695-1701.  
11839489 M.E.Newcomer (2002).
Protein folding and three-dimensional domain swapping: a strained relationship?
  Curr Opin Struct Biol, 12, 48-53.  
12379842 M.Kirsten Frank, F.Dyda, A.Dobrodumov, and A.M.Gronenborn (2002).
Core mutations switch monomeric protein GB1 into an intertwined tetramer.
  Nat Struct Biol, 9, 877-885.
PDB codes: 1mpe 1mvk
12163064 R.L.Dunbrack (2002).
Rotamer libraries in the 21st century.
  Curr Opin Struct Biol, 12, 431-440.  
12163066 W.P.Russ, and R.Ranganathan (2002).
Knowledge-based potential functions in protein design.
  Curr Opin Struct Biol, 12, 447-452.  
12021428 Y.Liu, and D.Eisenberg (2002).
3D domain swapping: as domains continue to swap.
  Protein Sci, 11, 1285-1299.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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