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PDBsum entry 1plc
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protein metals links
Electron transport PDB id
1plc

 

 

 

 

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Contents
Protein chain
99 a.a. *
Metals
_CU
Waters ×110
* Residue conservation analysis
PDB id:
1plc
Name: Electron transport
Title: Accuracy and precision in protein crystal structure analysis: restrained least-squares refinement of the crystal structure of poplar plastocyanin at 1.33 angstroms resolution
Structure: Plastocyanin. Chain: a. Engineered: yes
Source: Populus nigra. Organism_taxid: 3691
Resolution:
1.33Å     R-factor:   0.150    
Authors: J.M.Guss,H.C.Freeman
Key ref: J.M.Guss et al. (1992). Accuracy and precision in protein structure analysis: restrained least-squares refinement of the structure of poplar plastocyanin at 1.33 A resolution. Acta Crystallogr B, 48, 790-811. PubMed id: 1492962
Date:
11-Mar-92     Release date:   31-Oct-93    
Supersedes: 1pcy
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00299  (PLAS1_POPNI) -  Plastocyanin A, chloroplastic from Populus nigra
Seq:
Struc: 		168 a.a.
99 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
Acta Crystallogr B 48:790-811 (1992)
PubMed id: 1492962  
 
 
Accuracy and precision in protein structure analysis: restrained least-squares refinement of the structure of poplar plastocyanin at 1.33 A resolution.
J.M.Guss, H.D.Bartunik, H.C.Freeman.
 
  ABSTRACT  
 
The structure of the electron-transfer protein, plastocyanin (99 amino acids, one Cu atom, 10,500 Da) from poplar leaves, has been refined at 1.33 A resolution to a residual R = 0.15. The space group is orthorhombic, P2(1)2(1)2(1), a = 29.60 (1), b = 46.86 (3), c = 57.60 (3) A. The 14,303 reflections used in the refinement were obtained from a data set recorded on a four-circle diffractometer with radiation from a sealed fine-focus tube, combined with a data set measured on oscillation films exposed at the DESY synchrotron. The final model comprises 1442 (738 non-H) protein atoms, one Cu atom and 110 solvent molecules. Nine residues are described as disordered. The root-mean-square deviation from ideal bond lengths is 0.016 A and the root-mean-square difference between the positions of the C alpha atoms in this refined model and in the structure previously refined at 1.6 A resolution is 0.11 A. The effects of manual model adjustment, resolution, choice of standard values for geometrical parameters, inclusion of H atoms and inclusion of anomalous-scattering corrections on the copper-site geometry have been explored. The final values of the Cu-ligand bond lengths are: Cu--N(His37) 1.91, Cu--S(Cys84) 2.07, Cu--N(His87) 2.06, Cu--S(Met92) 2.82 A.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21054068 K.Ando (2010).
The axial methionine ligand may control the redox reorganizations in the active site of blue copper proteins.
  J Chem Phys, 133, 175101.  
19282479 S.Ghosh, X.Xie, A.Dey, Y.Sun, C.P.Scholes, and E.I.Solomon (2009).
Thermodynamic equilibrium between blue and green copper sites and the role of the protein in controlling function.
  Proc Natl Acad Sci U S A, 106, 4969-4974.  
18469078 K.Moritsugu, and J.C.Smith (2008).
REACH coarse-grained biomolecular simulation: transferability between different protein structural classes.
  Biophys J, 95, 1639-1648.  
18314973 Y.Zhang, and E.Oldfield (2008).
NMR hyperfine shifts in blue copper proteins: a quantum chemical investigation.
  J Am Chem Soc, 130, 3814-3823.  
16446449 D.F.Hansen, and J.J.Led (2006).
Determination of the geometric structure of the metal site in a blue copper protein by paramagnetic NMR.
  Proc Natl Acad Sci U S A, 103, 1738-1743.  
16432723 D.Flemming Hansen, S.I.Gorelsky, R.Sarangi, K.O.Hodgson, B.Hedman, H.E.Christensen, E.I.Solomon, and J.J.Led (2006).
Reinvestigation of the method used to map the electronic structure of blue copper proteins by NMR relaxation.
  J Biol Inorg Chem, 11, 277-285.  
16807974 E.I.Solomon, S.I.Gorelsky, and A.Dey (2006).
Metal-thiolate bonds in bioinorganic chemistry.
  J Comput Chem, 27, 1415-1428.  
16786065 K.Paraskevopoulos, M.Sundararajan, R.Surendran, M.A.Hough, R.R.Eady, I.H.Hillier, and S.S.Hasnain (2006).
Active site structures and the redox properties of blue copper proteins: atomic resolution structure of azurin II and electronic structure calculations of azurin, plastocyanin and stellacyanin.
  Dalton Trans, (), 3067-3076.
PDB code: 2ccw
15274913 J.Gough, and C.Chothia (2004).
The linked conservation of structure and function in a family of high diversity: the monomeric cupredoxins.
  Structure, 12, 917-925.  
15211513 L.L.Videau, W.B.Arendall, and J.S.Richardson (2004).
The cis-Pro touch-turn: a rare motif preferred at functional sites.
  Proteins, 56, 298-309.  
14652997 A.R.Bizzarri, B.Bonanni, G.Costantini, and S.Cannistraro (2003).
A combined atomic force microscopy and molecular dynamics simulation study on a plastocyanin mutant chemisorbed on a gold surface.
  Chemphyschem, 4, 1189-1195.  
12944318 E.L.Gross, and D.C.Pearson (2003).
Brownian dynamics simulations of the interaction of Chlamydomonas cytochrome f with plastocyanin and cytochrome c6.
  Biophys J, 85, 2055-2068.  
12039012 R.K.Szilagyi, and E.I.Solomon (2002).
Electronic structure and its relation to function in copper proteins.
  Curr Opin Chem Biol, 6, 250-258.  
  10975566 F.De Rienzo, R.R.Gabdoulline, M.C.Menziani, and R.C.Wade (2000).
Blue copper proteins: a comparative analysis of their molecular interaction properties.
  Protein Sci, 9, 1439-1454.  
10848961 X.S.Gong, J.Q.Wen, N.E.Fisher, S.Young, C.J.Howe, D.S.Bendall, and J.C.Gray (2000).
The role of individual lysine residues in the basic patch on turnip cytochrome f for electrostatic interactions with plastocyanin in vitro.
  Eur J Biochem, 267, 3461-3468.  
10024021 J.V.Lehtonen, K.Denessiouk, A.C.May, and M.S.Johnson (1999).
Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm.
  Proteins, 34, 341-355.  
10423449 R.Guzzi, L.Sportelli, C.La Rosa, D.Milardi, D.Grasso, M.P.Verbeet, and G.W.Canters (1999).
A spectroscopic and calorimetric investigation on the thermal stability of the Cys3Ala/Cys26Ala azurin mutant.
  Biophys J, 77, 1052-1063.  
9826593 D.C.Pearson, and E.L.Gross (1998).
Brownian dynamics study of the interaction between plastocyanin and cytochrome f.
  Biophys J, 75, 2698-2711.  
  9865961 M.H.Olsson, U.Ryde, and B.O.Roos (1998).
Quantum chemical calculations of the reorganization energy of blue-copper proteins.
  Protein Sci, 7, 2659-2668.  
9551554 M.Ubbink, M.Ejdebäck, B.G.Karlsson, and D.S.Bendall (1998).
The structure of the complex of plastocyanin and cytochrome f, determined by paramagnetic NMR and restrained rigid-body molecular dynamics.
  Structure, 6, 323-335.
PDB code: 2pcf
  9792096 Y.Xue, M.Okvist, O.Hansson, and S.Young (1998).
Crystal structure of spinach plastocyanin at 1.7 A resolution.
  Protein Sci, 7, 2099-2105.
PDB code: 1ag6
9746528 Z.Salamon, D.Huang, W.A.Cramer, and G.Tollin (1998).
Coupled plasmon-waveguide resonance spectroscopy studies of the cytochrome b6f/plastocyanin system in supported lipid bilayer membranes.
  Biophys J, 75, 1874-1885.  
9414237 G.M.Soriano, W.A.Cramer, and L.I.Krishtalik (1997).
Electrostatic effects on electron-transfer kinetics in the cytochrome f-plastocyanin complex.
  Biophys J, 73, 3265-3276.  
9183022 K.Sigfridsson, S.Young, and O.Hansson (1997).
Electron transfer between spinach plastocyanin mutants and photosystem 1.
  Eur J Biochem, 245, 805-812.  
8994588 L.W.Ungar, N.F.Scherer, and G.A.Voth (1997).
Classical molecular dynamics simulation of the photoinduced electron transfer dynamics of plastocyanin.
  Biophys J, 72, 5.  
8804589 D.C.Pearson, E.L.Gross, and E.S.David (1996).
Electrostatic properties of cytochrome f: implications for docking with plastocyanin.
  Biophys J, 71, 64-76.  
  8732753 J.A.Ybe, and M.H.Hecht (1996).
Sequence replacements in the central beta-turn of plastocyanin.
  Protein Sci, 5, 814-824.  
8816770 M.Gerstein, and C.Chothia (1996).
Packing at the protein-water interface.
  Proc Natl Acad Sci U S A, 93, 10167-10172.  
  8978664 M.Hippler, J.Reichert, M.Sutter, E.Zak, L.Altschmied, U.Schröer, R.G.Herrmann, and W.Haehnel (1996).
The plastocyanin binding domain of photosystem I.
  EMBO J, 15, 6374-6384.  
8954163 M.Ubbink, L.Y.Lian, S.Modi, P.A.Evans, and D.S.Bendall (1996).
Analysis of the 1H-NMR chemical shifts of Cu(I)-, Cu(II)- and Cd-substituted pea plastocyanin. Metal-dependent differences in the hydrogen-bond network around the copper site.
  Eur J Biochem, 242, 132-147.  
8673596 R.A.Capaldi (1996).
The complexity of a respiratory complex.
  Nat Struct Biol, 3, 570-574.  
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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