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PDBsum entry 1ejg
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Plant protein PDB id
1ejg

 

 

 

 

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Contents
Protein chain
48 a.a. *
* Residue conservation analysis
PDB id:
1ejg
Name: Plant protein
Title: Crambin at ultra-high resolution: valence electron density.
Structure: Crambin (pro22,ser22/leu25,ile25). Chain: a. Fragment: crambin
Source: Crambe hispanica subsp. Abyssinica. Organism_taxid: 3721. Strain: subsp. Abyssinica
Resolution:
0.54Å     R-factor:   0.090     R-free:   0.094
Authors: C.Jelsch,M.M.Teeter,V.Lamzin,V.Pichon-Lesme,B.Blessing,C.Lecomte
Key ref:
C.Jelsch et al. (2000). Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin. Proc Natl Acad Sci U S A, 97, 3171-3176. PubMed id: 10737790 DOI: 10.1073/pnas.97.7.3171
Date:
02-Mar-00     Release date:   05-Apr-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01542  (CRAM_CRAAB) -  Crambin from Crambe hispanica subsp. abyssinica
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)

 

 
DOI no: 10.1073/pnas.97.7.3171 Proc Natl Acad Sci U S A 97:3171-3176 (2000)
PubMed id: 10737790  
 
 
Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin.
C.Jelsch, M.M.Teeter, V.Lamzin, V.Pichon-Pesme, R.H.Blessing, C.Lecomte.
 
  ABSTRACT  
 
The charge density distribution of a protein has been refined experimentally. Diffraction data for a crambin crystal were measured to ultra-high resolution (0.54 A) at low temperature by using short-wavelength synchrotron radiation. The crystal structure was refined with a model for charged, nonspherical, multipolar atoms to accurately describe the molecular electron density distribution. The refined parameters agree within 25% with our transferable electron density library derived from accurate single crystal diffraction analyses of several amino acids and small peptides. The resulting electron density maps of redistributed valence electrons (deformation maps) compare quantitatively well with a high-level quantum mechanical calculation performed on a monopeptide. This study provides validation for experimentally derived parameters and a window into charge density analysis of biological macromolecules.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Ribbon diagram (16) showing the general fold of crambin. The disulfide bridges are shown in yellow. -sheet and extended chain are shown in green and the helices are red. 		Figure 2.
Fig. 2. Residual electron density in the peptide bond plane. (A) For the peptide Ala-9-Arg-10 when using a spherical neutral atom model, contour level 0.05 e^ /Å3. (B) Averaged over the 34 nondisordered peptides in crambin when using a spherical neutral atom model. (C) When using a multipolar charged atom model transferred from the database and (D) with average valence populations and multipoles refined, contour level 0.02 e^ /Å3. Positive: red lines; negative: blue lines.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21325717 J.M.Bąk, S.Domagała, C.Hübschle, C.Jelsch, B.Dittrich, and P.M.Dominiak (2011).
Verification of structural and electrostatic properties obtained by the use of different pseudoatom databases.
  Acta Crystallogr A, 67, 141-153.  
20516622 A.Higashiura, T.Kurakane, M.Matsuda, M.Suzuki, K.Inaka, M.Sato, T.Kobayashi, T.Tanaka, H.Tanaka, K.Fujiwara, and A.Nakagawa (2010).
High-resolution X-ray crystal structure of bovine H-protein at 0.88 A resolution.
  Acta Crystallogr D Biol Crystallogr, 66, 698-708.
PDB code: 3klr
20516624 L.Gabison, M.Chiadmi, M.El Hajji, B.Castro, N.Colloc'h, and T.Prangé (2010).
Near-atomic resolution structures of urate oxidase complexed with its substrate and analogues: the protonation state of the ligand.
  Acta Crystallogr D Biol Crystallogr, 66, 714-724.
PDB codes: 3l8w 3l9g 3lbg 3ld4
20567074 Z.Dauter, M.Jaskolski, and A.Wlodawer (2010).
Impact of synchrotron radiation on macromolecular crystallography: a personal view.
  J Synchrotron Radiat, 17, 433-444.  
19822758 A.Korostelev, M.Laurberg, and H.F.Noller (2009).
Multistart simulated annealing refinement of the crystal structure of the 70S ribosome.
  Proc Natl Acad Sci U S A, 106, 18195-18200.  
19101147 A.Leis, B.Rockel, L.Andrees, and W.Baumeister (2009).
Visualizing cells at the nanoscale.
  Trends Biochem Sci, 34, 60-70.  
19562114 D.Bang, V.Tereshko, A.A.Kossiakoff, and S.B.Kent (2009).
Role of a salt bridge in the model protein crambin explored by chemical protein synthesis: X-ray structure of a unique protein analogue, [V15A]crambin-alpha-carboxamide.
  Mol Biosyst, 5, 750-756.
PDB codes: 2fd7 2fd9
19066990 J.J.Stewart (2009).
Application of the PM6 method to modeling proteins.
  J Mol Model, 15, 765-805.  
19690373 M.J.Schnieders, T.D.Fenn, V.S.Pande, and A.T.Brunger (2009).
Polarizable atomic multipole X-ray refinement: application to peptide crystals.
  Acta Crystallogr D Biol Crystallogr, 65, 952-965.  
18814299 P.Labute (2009).
Protonate3D: assignment of ionization states and hydrogen coordinates to macromolecular structures.
  Proteins, 75, 187-205.  
19237751 S.K.Johnas, B.Dittrich, A.Meents, M.Messerschmidt, and E.F.Weckert (2009).
Charge-density study on cyclosporine A.
  Acta Crystallogr D Biol Crystallogr, 65, 284-293.  
18274526 A.J.Dingley, L.Nisius, F.Cordier, and S.Grzesiek (2008).
Direct detection of N-H[...]N hydrogen bonds in biomolecules by NMR spectroscopy.
  Nat Protoc, 3, 242-248.  
18453693 B.Guillot, C.Jelsch, A.Podjarny, and C.Lecomte (2008).
Charge-density analysis of a protein structure at subatomic resolution: the human aldose reductase case.
  Acta Crystallogr D Biol Crystallogr, 64, 567-588.  
18421138 C.Lecomte, C.Jelsch, B.Guillot, B.Fournier, and A.Lagoutte (2008).
Ultrahigh-resolution crystallography and related electron density and electrostatic properties in proteins.
  J Synchrotron Radiat, 15, 202-203.  
18323618 E.Nishibori, T.Nakamura, M.Arimoto, S.Aoyagi, H.Ago, M.Miyano, T.Ebisuzaki, and M.Sakata (2008).
Application of maximum-entropy maps in the accurate refinement of a putative acylphosphatase using 1.3 A X-ray diffraction data.
  Acta Crystallogr D Biol Crystallogr, 64, 237-247.  
18305196 N.Juranić, J.J.Dannenberg, G.Cornilescu, P.Salvador, E.Atanasova, H.C.Ahn, S.Macura, J.L.Markley, and F.G.Prendergast (2008).
Structural dependencies of protein backbone 2JNC' couplings.
  Protein Sci, 17, 768-776.  
17242509 A.Volkov, M.Messerschmidt, and P.Coppens (2007).
Improving the scattering-factor formalism in protein refinement: application of the University at Buffalo Aspherical-Atom Databank to polypeptide structures.
  Acta Crystallogr D Biol Crystallogr, 63, 160-170.  
18078545 C.D.Putnam, M.Hammel, G.L.Hura, and J.A.Tainer (2007).
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.
  Q Rev Biophys, 40, 191-285.  
17664653 C.J.Burden, and A.J.Oakley (2007).
Anisotropic atomic motions in high-resolution protein crystallography molecular dynamics simulations.
  Phys Biol, 4, 79-90.  
18084073 J.Wang, M.Dauter, R.Alkire, A.Joachimiak, and Z.Dauter (2007).
Triclinic lysozyme at 0.65 A resolution.
  Acta Crystallogr D Biol Crystallogr, 63, 1254-1268.
PDB code: 2vb1
17452786 M.Jaskolski, M.Gilski, Z.Dauter, and A.Wlodawer (2007).
Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them?
  Acta Crystallogr D Biol Crystallogr, 63, 611-620.  
17567747 N.Juranić, E.Atanasova, J.H.Streiff, S.Macura, and F.G.Prendergast (2007).
Solvent-induced differentiation of protein backbone hydrogen bonds in calmodulin.
  Protein Sci, 16, 1329-1337.  
18157846 N.R.Skrynnikov (2007).
Asymmetric doublets in MAS NMR: coherent and incoherent mechanisms.
  Magn Reson Chem, 45, S161-S173.  
18019525 P.Luger (2007).
Fast electron density methods in the life sciences--a routine application in the future?
  Org Biomol Chem, 5, 2529-2540.  
18007035 P.V.Afonine, R.W.Grosse-Kunstleve, P.D.Adams, V.Y.Lunin, and A.Urzhumtsev (2007).
On macromolecular refinement at subatomic resolution with interatomic scatterers.
  Acta Crystallogr D Biol Crystallogr, 63, 1194-1197.  
16707576 A.K.Katz, X.Li, H.L.Carrell, B.L.Hanson, P.Langan, L.Coates, B.P.Schoenborn, J.P.Glusker, and G.J.Bunick (2006).
Locating active-site hydrogen atoms in D-xylose isomerase: time-of-flight neutron diffraction.
  Proc Natl Acad Sci U S A, 103, 8342-8347.
PDB codes: 2glk 2gub 2gve
17057335 B.Dittrich, C.B.Hübschle, P.Luger, and M.A.Spackman (2006).
Introduction and validation of an invariom database for amino-acid, peptide and protein molecules.
  Acta Crystallogr D Biol Crystallogr, 62, 1325-1335.  
16639756 D.Bang, B.L.Pentelute, and S.B.Kent (2006).
Kinetically controlled ligation for the convergent chemical synthesis of proteins.
  Angew Chem Int Ed Engl, 45, 3985-3988.  
16460145 F.Furche, and J.P.Perdew (2006).
The performance of semilocal and hybrid density functionals in 3d transition-metal chemistry.
  J Chem Phys, 124, 044103.  
16569017 H.C.Ahn, N.Juranić, S.Macura, and J.L.Markley (2006).
Three-dimensional structure of the water-insoluble protein crambin in dodecylphosphocholine micelles and its minimal solvent-exposed surface.
  J Am Chem Soc, 128, 4398-4404.
PDB codes: 1yv8 1yva 2eya 2eyb 2eyc 2eyd
16552136 J.Hakanpää, M.Linder, A.Popov, A.Schmidt, and J.Rouvinen (2006).
Hydrophobin HFBII in detail: ultrahigh-resolution structure at 0.75 A.
  Acta Crystallogr D Biol Crystallogr, 62, 356-367.
PDB code: 2b97
16500987 K.A.Walther, J.Brujić, H.Li, and J.M.Fernández (2006).
Sub-angstrom conformational changes of a single molecule captured by AFM variance analysis.
  Biophys J, 90, 3806-3812.  
17132861 N.Yu, X.Li, G.Cui, S.A.Hayik, and K.M.Merz (2006).
Critical assessment of quantum mechanics based energy restraints in protein crystal structure refinement.
  Protein Sci, 15, 2773-2784.  
17013680 T.Wang, D.S.Weaver, S.Cai, and E.R.Zuiderweg (2006).
Quantifying Lipari-Szabo modelfree parameters from 13CO NMR relaxation experiments.
  J Biomol NMR, 36, 79.  
15983423 H.Bönisch, C.L.Schmidt, P.Bianco, and R.Ladenstein (2005).
Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 A X-ray structure of mutant W4L/R5S.
  Acta Crystallogr D Biol Crystallogr, 61, 990.
PDB codes: 1yk4 1yk5
15608379 K.V.Dunlop, R.T.Irvin, and B.Hazes (2005).
Pros and cons of cryocrystallography: should we also collect a room-temperature data set?
  Acta Crystallogr D Biol Crystallogr, 61, 80-87.
PDB codes: 1x6p 1x6q 1x6r 1x6x 1x6y 1x6z
15735343 N.Yu, H.P.Yennawar, and K.M.Merz (2005).
Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics.
  Acta Crystallogr D Biol Crystallogr, 61, 322-332.  
16084753 P.B.Pelegrini, and O.L.Franco (2005).
Plant gamma-thionins: novel insights on the mechanism of action of a multi-functional class of defense proteins.
  Int J Biochem Cell Biol, 37, 2239-2253.  
15507748 A.Volkov, T.Koritsanszky, X.Li, and P.Coppens (2004).
Response to the paper A comparison between experimental and theoretical aspherical-atom scattering factors for charge-density refinement of large molecules, by Pichon-Pesme, Jelsch, Guillot & Lecomte (2004).
  Acta Crystallogr A, 60, 638-639.  
15613085 B.Stec, O.Markman, U.Rao, G.Heffron, S.Henderson, L.P.Vernon, V.Brumfeld, and M.M.Teeter (2004).
Proposal for molecular mechanism of thionins deduced from physico-chemical studies of plant toxins.
  J Pept Res, 64, 210-224.  
15146478 E.I.Howard, R.Sanishvili, R.E.Cachau, A.Mitschler, B.Chevrier, P.Barth, V.Lamour, M.Van Zandt, E.Sibley, C.Bon, D.Moras, T.R.Schneider, A.Joachimiak, and A.Podjarny (2004).
Ultrahigh resolution drug design I: details of interactions in human aldose reductase-inhibitor complex at 0.66 A.
  Proteins, 55, 792-804.
PDB code: 1us0
14747702 P.V.Afonine, V.Y.Lunin, N.Muzet, and A.Urzhumtsev (2004).
On the possibility of the observation of valence electron density for individual bonds in proteins in conventional difference maps.
  Acta Crystallogr D Biol Crystallogr, 60, 260-274.  
12557191 J.P.Linge, M.A.Williams, C.A.Spronk, A.M.Bonvin, and M.Nilges (2003).
Refinement of protein structures in explicit solvent.
  Proteins, 50, 496-506.  
12937341 N.Engler, A.Ostermann, N.Niimura, and F.G.Parak (2003).
Hydrogen atoms in proteins: positions and dynamics.
  Proc Natl Acad Sci U S A, 100, 10243-10248.  
12855766 N.Muzet, B.Guillot, C.Jelsch, E.Howard, and C.Lecomte (2003).
Electrostatic complementarity in an aldose reductase complex from ultra-high-resolution crystallography and first-principles calculations.
  Proc Natl Acad Sci U S A, 100, 8742-8747.  
14714388 P.Ilich, and N.Juranić (2003).
One-bond 15N-13C' nuclear spin-spin coupling in N-methylacetamide: a model for hydrogen-bonded peptides.
  Chemphyschem, 4, 1358-1360.  
12547803 T.P.Ko, H.Robinson, Y.G.Gao, C.H.Cheng, A.L.DeVries, and A.H.Wang (2003).
The refined crystal structure of an eel pout type III antifreeze protein RD1 at 0.62-A resolution reveals structural microheterogeneity of protein and solvation.
  Biophys J, 84, 1228-1237.
PDB code: 1ucs
12011434 A.Grishaev, and M.Llinas (2002).
Protein structure elucidation from NMR proton densities.
  Proc Natl Acad Sci U S A, 99, 6713-6718.  
11943548 C.Mattos (2002).
Protein-water interactions in a dynamic world.
  Trends Biochem Sci, 27, 203-208.  
12198301 R.Thaimattam, E.Tykarska, A.Bierzynski, G.M.Sheldrick, and M.Jaskolski (2002).
Atomic resolution structure of squash trypsin inhibitor: unexpected metal coordination.
  Acta Crystallogr D Biol Crystallogr, 58, 1448-1461.
PDB code: 1lu0
11572978 M.M.Teeter, A.Yamano, B.Stec, and U.Mohanty (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.
PDB codes: 1jxt 1jxu 1jxw 1jxx 1jxy
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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