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PDBsum entry 2jhs
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Inhibitor PDB id
2jhs

 

 

 

 

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Contents
Protein chain
137 a.a. *
Ligands
FLC
Waters ×133
* Residue conservation analysis
PDB id:
2jhs
Name: Inhibitor
Title: Crystal structure of rhogdi k135h,k138h,k141h mutant
Structure: Rho gdp-dissociation inhibitor 1. Chain: a. Fragment: isoprenyl-binding domain, residues 66-201. Synonym: rho gdi 1, rho-gdi alpha. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
1.95Å     R-factor:   0.179     R-free:   0.209
Authors: D.R.Cooper,M.Zawadzki,Z.S.Derewenda
Key ref:
D.R.Cooper et al. (2007). Protein crystallization by surface entropy reduction: optimization of the SER strategy. Acta Crystallogr D Biol Crystallogr, 63, 636-645. PubMed id: 17452789 DOI: 10.1107/S0907444907010931
Date:
23-Feb-07     Release date:   08-May-07    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P52565  (GDIR1_HUMAN) -  Rho GDP-dissociation inhibitor 1 from Homo sapiens
Seq:
Struc: 		204 a.a.
137 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 

 
DOI no: 10.1107/S0907444907010931 Acta Crystallogr D Biol Crystallogr 63:636-645 (2007)
PubMed id: 17452789  
 
 
Protein crystallization by surface entropy reduction: optimization of the SER strategy.
D.R.Cooper, T.Boczek, K.Grelewska, M.Pinkowska, M.Sikorska, M.Zawadzki, Z.Derewenda.
 
  ABSTRACT  
 
A strategy of rationally engineering protein surfaces with the aim of obtaining mutants that are distinctly more susceptible to crystallization than the wild-type protein has previously been suggested. The strategy relies on replacing small clusters of two to three surface residues characterized by high conformational entropy with alanines. This surface entropy reduction (or SER) method has proven to be an effective salvage pathway for proteins that are difficult to crystallize. Here, a systematic comparison of the efficacy of using Ala, His, Ser, Thr and Tyr to replace high-entropy residues is reported. A total of 40 mutants were generated and screened using two different procedures. The results reaffirm that alanine is a particularly good choice for a replacement residue and identify tyrosines and threonines as additional candidates that have considerable potential to mediate crystal contacts. The propensity of these mutants to form crystals in alternative screens in which the normal crystallization reservoir solutions were replaced with 1.5 M NaCl was also examined. The results were impressive: more than half of the mutants yielded a larger number of crystals with salt as the reservoir solution. This method greatly increased the variety of conditions that yielded crystals. Taken together, these results suggest a powerful crystallization strategy that combines surface engineering with efficient screening using standard and alternate reservoir solutions.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 The distribution of the mutations used in this study. The mutation clusters were designated by a single letter A-I. The mutations corresponding to each cluster are shown as magenta spheres on the ribbon diagram. A cartoon representation of RhoGDI is shown for reference. 		Figure 4.
Figure 4 Histogram of hits in the salt screens.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 636-645) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21217145 J.C.Pai, J.A.Culver, J.E.Drury, R.S.Motani, R.L.Lieberman, and J.A.Maynard (2011).
Conversion of scFv peptide-binding specificity for crystal chaperone development.
  Protein Eng Des Sel, 24, 419-428.  
20673774 R.E.Hubbard (2011).
Structure-based drug discovery and protein targets in the CNS.
  Neuropharmacology, 60, 7.  
21460442 Z.S.Derewenda (2011).
It's all in the crystals….
  Acta Crystallogr D Biol Crystallogr, 67, 243-248.  
  20208147 D.R.Cooper, K.Grelewska, C.Y.Kim, A.Joachimiak, and Z.S.Derewenda (2010).
The structure of DinB from Geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamily.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 219-224.
PDB code: 3gor
20506323 P.Sledz, H.Zheng, K.Murzyn, M.Chruszcz, M.D.Zimmerman, M.D.Chordia, A.Joachimiak, and W.Minor (2010).
New surface contacts formed upon reductive lysine methylation: improving the probability of protein crystallization.
  Protein Sci, 19, 1395-1404.  
20862670 P.Sun, B.P.Austin, J.Tözsér, and D.S.Waugh (2010).
Structural determinants of tobacco vein mottling virus protease substrate specificity.
  Protein Sci, 19, 2240-2251.
PDB code: 3mmg
20213425 W.H.Eschenfeldt, N.Maltseva, L.Stols, M.I.Donnelly, M.Gu, B.Nocek, K.Tan, Y.Kim, and A.Joachimiak (2010).
Cleavable C-terminal His-tag vectors for structure determination.
  J Struct Funct Genomics, 11, 31-39.  
20127187 Y.Fan, and A.Joachimiak (2010).
Enhanced crystal packing due to solvent reorganization through reductive methylation of lysine residues in oxidoreductase from Streptococcus pneumoniae.
  J Struct Funct Genomics, 11, 101-111.  
20445236 Z.S.Derewenda (2010).
Application of protein engineering to enhance crystallizability and improve crystal properties.
  Acta Crystallogr D Biol Crystallogr, 66, 604-615.  
19489729 A.Edwards (2009).
Large-scale structural biology of the human proteome.
  Annu Rev Biochem, 78, 541-568.  
19765976 A.Joachimiak (2009).
High-throughput crystallography for structural genomics.
  Curr Opin Struct Biol, 19, 573-584.  
19292479 J.J.Lavinder, S.B.Hari, B.J.Sullivan, and T.J.Magliery (2009).
High-throughput thermal scanning: a general, rapid dye-binding thermal shift screen for protein engineering.
  J Am Chem Soc, 131, 3794-3795.  
19505478 J.R.Partridge, and T.U.Schwartz (2009).
Crystallographic and biochemical analysis of the Ran-binding zinc finger domain.
  J Mol Biol, 391, 375-389.
PDB codes: 3gj0 3gj3 3gj4 3gj5 3gj6 3gj7 3gj8
19646256 L.Kurgan, A.A.Razib, S.Aghakhani, S.Dick, M.Mizianty, and S.Jahandideh (2009).
CRYSTALP2: sequence-based protein crystallization propensity prediction.
  BMC Struct Biol, 9, 50.  
  19298050 S.Koide, and S.S.Sidhu (2009).
The importance of being tyrosine: lessons in molecular recognition from minimalist synthetic binding proteins.
  ACS Chem Biol, 4, 325-334.  
  19342785 T.Shimamura, Y.Nitanai, T.Uchiyama, and H.Matsuzawa (2009).
Improvement of crystal quality by surface mutations of beta-lactamase Toho-1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 379-382.
PDB code: 2zq8
19860716 W.F.Anderson (2009).
Structural genomics and drug discovery for infectious diseases.
  Infect Disord Drug Targets, 9, 507-517.  
19079241 W.N.Price, Y.Chen, S.K.Handelman, H.Neely, P.Manor, R.Karlin, R.Nair, J.Liu, M.Baran, J.Everett, S.N.Tong, F.Forouhar, S.S.Swaminathan, T.Acton, R.Xiao, J.R.Luft, A.Lauricella, G.T.DeTitta, B.Rost, G.T.Montelione, and J.F.Hunt (2009).
Understanding the physical properties that control protein crystallization by analysis of large-scale experimental data.
  Nat Biotechnol, 27, 51-57.  
19575413 Y.Wine, N.Cohen-Hadar, R.Lamed, A.Freeman, and F.Frolow (2009).
Modification of protein crystal packing by systematic mutations of surface residues: implications on biotemplating and crystal porosity.
  Biotechnol Bioeng, 104, 444-457.  
18235432 B.G.Fox, C.Goulding, M.G.Malkowski, L.Stewart, and A.Deacon (2008).
Structural genomics: from genes to structures with valuable materials and many questions in between.
  Nat Methods, 5, 129-132.  
18448325 E.D.Levy, and J.B.Pereira-Leal (2008).
Evolution and dynamics of protein interactions and networks.
  Curr Opin Struct Biol, 18, 349-357.  
  18607092 L.Rodríguez-Fernández, F.J.López-Jaramillo, A.Bacher, M.Fischer, and S.Weinkauf (2008).
Improvement of the quality of lumazine synthase crystals by protein engineering.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 625-628.  
18022192 M.E.Yanez, K.V.Korotkov, J.Abendroth, and W.G.Hol (2008).
The crystal structure of a binary complex of two pseudopilins: EpsI and EpsJ from the type 2 secretion system of Vibrio vulnificus.
  J Mol Biol, 375, 471-486.
PDB code: 2ret
18782772 M.H.Kim, Y.Kim, H.J.Park, J.S.Lee, S.N.Kwak, W.H.Jung, S.G.Lee, D.Kim, Y.C.Lee, and T.K.Oh (2008).
Structural Insight into Bioremediation of Triphenylmethane Dyes by Citrobacter sp. Triphenylmethane Reductase.
  J Biol Chem, 283, 31981-31990.
PDB codes: 2jl1 2vrb 2vrc
  18931446 M.Senda, S.Muto, M.Horikoshi, and T.Senda (2008).
Effect of leucine-to-methionine substitutions on the diffraction quality of histone chaperone SET/TAF-Ibeta/INHAT crystals.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 960-965.  
  18084085 B.Liu, V.M.Luna, Y.Chen, C.D.Stout, and J.A.Fee (2007).
An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from Thermus thermophilus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 1029-1034.
PDB codes: 2qpd 2qpe
  17909291 J.Wickham, and S.T.Walsh (2007).
Crystallization and preliminary X-ray diffraction of human interleukin-7 bound to unglycosylated and glycosylated forms of its alpha-receptor.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 865-869.  
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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