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PDBsum entry 1jxy

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Plant protein PDB id
1jxy
Jmol
Contents
Protein chain
48 a.a. *
Ligands
EOH
* Residue conservation analysis
PDB id:
1jxy
Name: Plant protein
Title: Crambin mixed sequence form at 220 k. Protein/water substate
Structure: Crambin. Chain: a
Source: Crambe hispanica subsp. Abyssinica. Organism_taxid: 3721. Strain: subsp. Abyssinica
Resolution:
0.89Å     R-factor:   0.145    
Authors: M.M.Teeter,A.Yamano,B.Stec,U.Mohanty
Key ref:
M.M.Teeter et al. (2001). On the nature of a glassy state of matter in a hydrated protein: Relation to protein function. Proc Natl Acad Sci U S A, 98, 11242-11247. PubMed id: 11572978 DOI: 10.1073/pnas.201404398
Date:
10-Sep-01     Release date:   31-Oct-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01542  (CRAM_CRAAB) -  Crambin
Seq:
Struc:
46 a.a.
48 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     defense response   1 term 

 

 
DOI no: 10.1073/pnas.201404398 Proc Natl Acad Sci U S A 98:11242-11247 (2001)
PubMed id: 11572978  
 
 
On the nature of a glassy state of matter in a hydrated protein: Relation to protein function.
M.M.Teeter, A.Yamano, B.Stec, U.Mohanty.
 
  ABSTRACT  
 
Diverse biochemical and biophysical experiments indicate that all proteins, regardless of size or origin, undergo a dynamic transition near 200 K. The cause of this shift in dynamic behavior, termed a "glass transition," and its relation to protein function are important open questions. One explanation postulated for the transition is solidification of correlated motions in proteins below the transition. We verified this conjecture by showing that crambin's radius of gyration (Rg) remains constant below approximately 180 K. We show that both atom position and dynamics of protein and solvent are physically coupled, leading to a novel cooperative state. This glassy state is identified by negative slopes of the Debye-Waller (B) factor vs. temperature. It is composed of multisubstate side chains and solvent. Based on generalization of Adam-Gibbs' notion of a cooperatively rearranging region and decrease of the total entropy with temperature, we calculate the slope of the Debye-Waller factor. The results are in accord with experiment.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. A and B substates of the Asn-12 side chain in crambin coupled to the A and B water networks at 130 K. Note that the electron density for the water A and B substates are well separated for W105 and W119. Hydrogen bonds drawn as dotted lines are all between 2.75 and 3.11 Å. Electron density (2F[o] F[c]) is contoured at the 2 level.
Figure 2.
Fig. 2. Water rings in crambin at 160 K. (a) A stereodiagram of the extensive network of water rings from the largest crystal solvent region. Single letter codes (T = Thr, P = Pro, D = Asp) are used for the protein and symmetry-related molecules (residues with # after their number.) Electron density (2F[o] F[c]) is contoured at the 1.5 level. Water-water hydrogen bonds, as well as protein bonds, are shown in thick lines. One pentagon ring at the left (114BO-116BO-142O-165O-99O) is repeated at the right for 2-fold-screw-axis related waters (#). Water molecules with B in their label indicate that the ring arrays shown here are for the B substate and have partial occupancy. This cluster of rings contains two pentagon rings, three hexagon rings, and one heptagon ring. Hexagons can adopt a chair conformation when two waters in the ring hydrogen bond to the same carbonyl (97O# and 150#). Electron density (2F[o] F[c]) is contoured at the 1.5 level. (b) Number of rings vs. temperature for crambin water molecules in the largest water region. The number of rings is plotted for 130 K, 160 K, 200 K, 220 K, and 293 K. Pentagons are represented by filled triangles, hexagons by shaded squares, and heptagons by open circles. At 293 K, the remaining pentagons cluster near Leu-18 (37). Note that data for 160 K, 200 K, 220 K, and 240 K are on the same crystal.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21472814 E.I.Howard, M.P.Blakeley, M.Haertlein, I.P.Haertlein, A.Mitschler, S.J.Fisher, A.C.Siah, A.G.Salvay, A.Popov, C.M.Dieckmann, T.Petrova, and A.Podjarny (2011).
Neutron structure of type-III antifreeze protein allows the reconstruction of AFP-ice interface.
  J Mol Recognit, 24, 724-732.
PDB code: 3qf6
20012211 M.Warkentin, and R.E.Thorne (2010).
Slow cooling and temperature-controlled protein crystallography.
  J Struct Funct Genomics, 11, 85-89.  
20382997 M.Weik, and J.P.Colletier (2010).
Temperature-dependent macromolecular X-ray crystallography.
  Acta Crystallogr D Biol Crystallogr, 66, 437-446.  
19883599 F.Meersman, D.Bowron, A.K.Soper, and M.H.Koch (2009).
Counteraction of urea by trimethylamine N-oxide is due to direct interaction.
  Biophys J, 97, 2559-2566.  
19774277 P.K.Verma, A.Makhal, R.K.Mitra, and S.K.Pal (2009).
Role of solvation dynamics in the kinetics of solvolysis reactions in microreactors.
  Phys Chem Chem Phys, 11, 8467-8476.  
19067520 V.S.Bajaj, P.C.van der Wel, and R.G.Griffin (2009).
Observation of a low-temperature, dynamically driven structural transition in a polypeptide by solid-state NMR spectroscopy.
  J Am Chem Soc, 131, 118-128.  
17719000 C.Mattos, and A.C.Clark (2008).
Minimizing frustration by folding in an aqueous environment.
  Arch Biochem Biophys, 469, 118-131.  
18586843 D.Zhang, H.Lans, W.Vermeulen, A.Lenferink, and C.Otto (2008).
Quantitative fluorescence correlation spectroscopy reveals a 1000-fold increase in lifetime of protein functionality.
  Biophys J, 95, 3439-3446.  
18775960 N.Sengupta, S.Jaud, and D.J.Tobias (2008).
Hydration dynamics in a partially denatured ensemble of the globular protein human alpha-lactalbumin investigated with molecular dynamics simulations.
  Biophys J, 95, 5257-5267.  
18351810 P.S.Sarangapani, and Y.Zhu (2008).
Impeded structural relaxation of a hard-sphere colloidal suspension under confinement.
  Phys Rev E Stat Nonlin Soft Matter Phys, 77, 010501.  
18990783 Y.Zhang, and W.O.Handcock (2008).
Retraction.
  Biophys J, 95, 3521.  
17881830 B.Stec (2007).
Comment on Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them? by Jaskolski, Gilski, Dauter & Wlodawer (2007).
  Acta Crystallogr D Biol Crystallogr, 63, 1113-1114.  
17986611 K.Wood, M.Plazanet, F.Gabel, B.Kessler, D.Oesterhelt, D.J.Tobias, G.Zaccai, and M.Weik (2007).
Coupling of protein and hydration-water dynamics in biological membranes.
  Proc Natl Acad Sci U S A, 104, 18049-18054.  
17416616 L.D'Alfonso, M.Collini, F.Cannone, G.Chirico, B.Campanini, G.Cottone, and L.Cordone (2007).
GFP-mut2 proteins in trehalose-water matrixes: spatially heterogeneous protein-water-sugar structures.
  Biophys J, 93, 284-293.  
17131430 V.Helms (2007).
Protein dynamics tightly connected to the dynamics of surrounding and internal water molecules.
  Chemphyschem, 8, 23-33.  
17155105 N.Nakagawa, and M.Peyrard (2006).
Modeling protein thermodynamics and fluctuations at the mesoscale.
  Phys Rev E Stat Nonlin Soft Matter Phys, 74, 041916.  
16790934 N.Watanabe, T.Akiba, R.Kanai, and K.Harata (2006).
Structure of an orthorhombic form of xylanase II from Trichoderma reesei and analysis of thermal displacement.
  Acta Crystallogr D Biol Crystallogr, 62, 784-792.
PDB codes: 2dfb 2dfc
17155508 P.Kumar, Z.Yan, L.Xu, M.G.Mazza, S.V.Buldyrev, S.H.Chen, S.Sastry, and H.E.Stanley (2006).
Glass transition in biomolecules and the liquid-liquid critical point of water.
  Phys Rev Lett, 97, 177802.  
16942221 S.A.Dzuba, E.P.Kirilina, and E.S.Salnikov (2006).
On the possible manifestation of harmonic-anharmonic dynamical transition in glassy media in electron paramagnetic resonance of nitroxide spin probes.
  J Chem Phys, 125, 054502.  
16852609 D.Russo, R.K.Murarka, J.R.Copley, and T.Head-Gordon (2005).
Molecular view of water dynamics near model peptides.
  J Phys Chem B, 109, 12966-12975.  
15051877 B.Halle (2004).
Biomolecular cryocrystallography: structural changes during flash-cooling.
  Proc Natl Acad Sci U S A, 101, 4793-4798.  
15169050 J.C.Dyre, and N.B.Olsen (2004).
Landscape equivalent of the shoving model.
  Phys Rev E Stat Nonlin Soft Matter Phys, 69, 042501.  
14739317 M.M.Teeter (2004).
Myoglobin cavities provide interior ligand pathway.
  Protein Sci, 13, 313-318.  
15111430 M.Weik, X.Vernede, A.Royant, and D.Bourgeois (2004).
Temperature derivative fluorescence spectroscopy as a tool to study dynamical changes in protein crystals.
  Biophys J, 86, 3176-3185.  
15345526 T.Becker, J.A.Hayward, J.L.Finney, R.M.Daniel, and J.C.Smith (2004).
Neutron frequency windows and the protein dynamical transition.
  Biophys J, 87, 1436-1444.  
12944299 A.L.Tournier, J.Xu, and J.C.Smith (2003).
Translational hydration water dynamics drives the protein glass transition.
  Biophys J, 85, 1871-1875.  
12961983 F.R.Salsbury, W.G.Han, L.Noodleman, and C.L.Brooks (2003).
Temperature-dependent behavior of protein-chromophore interactions: a theoretical study of a blue fluorescent antibody.
  Chemphyschem, 4, 848-855.  
12124295 A.Paciaroni, S.Cinelli, and G.Onori (2002).
Effect of the environment on the protein dynamical transition: a neutron scattering study.
  Biophys J, 83, 1157-1164.  
11943548 C.Mattos (2002).
Protein-water interactions in a dynamic world.
  Trends Biochem Sci, 27, 203-208.  
11955127 M.Tarek, and D.J.Tobias (2002).
Role of protein-water hydrogen bond dynamics in the protein dynamical transition.
  Phys Rev Lett, 88, 138101.  
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.