9PCY

HIGH-RESOLUTION SOLUTION STRUCTURE OF REDUCED FRENCH BEAN PLASTOCYANIN AND COMPARISON WITH THE CRYSTAL STRUCTURE OF POPLAR PLASTOCYANIN


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 16 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High-resolution solution structure of reduced French bean plastocyanin and comparison with the crystal structure of poplar plastocyanin.

Moore, J.M.Lepre, C.A.Gippert, G.P.Chazin, W.J.Case, D.A.Wright, P.E.

(1991) J.Mol.Biol. 221: 533-555


  • PubMed Abstract: 
  • The three-dimensional solution structure of reduced (CuI) plastocyanin from French bean leaves has been determined by distance geometry and restrained molecular dynamics methods using constraints obtained from 1H n.m.r. (nuclear magnetic resonance) s ...

    The three-dimensional solution structure of reduced (CuI) plastocyanin from French bean leaves has been determined by distance geometry and restrained molecular dynamics methods using constraints obtained from 1H n.m.r. (nuclear magnetic resonance) spectroscopy. A total of 1244 experimental constraints were used, including 1120 distance constraints, 103 dihedral angle constraints and 21 hydrogen bond constraints. Stereospecific assignments were made for 26 methylene groups and the methyls of 11 valines. Additional constraints on copper co-ordination were included in the restrained dynamics calculations. The structures are well defined with average atomic root-mean-square deviations from the mean of 0.45 A for all backbone heavy atoms and 1.08 A for side-chain heavy atoms. French bean plastocyanin adopts a beta-sandwich structure in solution that is similar to the X-ray structure of reduced poplar plastocyanin; the average atomic root-mean-square difference between 16 n.m.r. structures and the X-ray structure is 0.76 A for all backbone heavy atoms. The conformations of the side-chains that constitute the hydrophobic core of French bean plastocyanin are very well defined. Of 47 conserved residues that populate a single chi 1 angle in solution, 43 have the same rotamer in the X-ray structure. Many surface side-chains adopt highly preferred conformations in solution, although the 3J alpha beta coupling constants often indicate some degree of conformational averaging. Some surface side-chains are disordered in both the solution and crystal structures of plastocyanin. There is a striking correlation between measures of side-chain disorder in solution and side-chain temperature factors in the X-ray structure. Side-chains that form a distinctive acidic surface region, believed to be important in binding other electron transfer proteins, appear to be disordered. Fifty backbone amide protons form hydrogen bonds to carbonyls in more than 60% of the n.m.r. structures; 45 of these amide protons exchange slowly with solvent deuterons. Ten hydrogen bonds are formed between side-chain and backbone atoms, eight of which are correlated with decreased proton exchange. Of the 60 hydrogen bonds formed in French bean plastocyanin, 56 occur in the X-ray structure of the poplar protein; two of the missing hydrogen bonds are absent as a result of mutations. It appears that molecular dynamics refinement of highly constrained n.m.r. structures allows accurate prediction of the pattern of hydrogen bonding.


    Related Citations: 
    • Computational Methods for Determining Protein Structures from NMR Data
      Gippert, G.P.,Yip, P.F.,Wright, P.E.,Case, D.A.
      (1990) Biochem.Pharm. 40: 15
    • Complete Assignment of the 1H Nuclear Magnetic Resonance Spectrum of French Bean Plastocyanin. Application of an Integrated Approach to Spin System Identification in Proteins
      Chazin, W.J.,Rance, M.,Wright, P.E.
      (1988) J.Mol.Biol. 202: 603
    • Complete Assignment of the 1H Nuclear Magnetic Resonance Spectrum of French Bean Plastocyanin. Sequential Resonance Assignments, Secondary Structure and Global Fold
      Chazin, W.J.,Wright, P.E.
      (1988) J.Mol.Biol. 202: 623
    • Three-Dimensional Solution Structure of Plastocyanin from the Green Alga Scenedesmus Obliquus
      Moore, J.M.,Case, D.A.,Chazin, W.J.,Gippert, G.P.,Havel, T.F.,Powls, R.,Wright, P.E.
      (1988) Science 240: 314


    Organizational Affiliation

    Department of Molecular Biology, Research Institute of Scripps Clinic, La Jolla, CA 92037.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PLASTOCYANIN
A
99Phaseolus vulgarisMutation(s): 0 
Gene Names: PETE
Find proteins for P00287 (Phaseolus vulgaris)
Go to UniProtKB:  P00287
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 16 
  • Olderado: 9PCY Olderado
Software Package:
Software NamePurpose
AMBERrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance