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PDBsum entry 3cti
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Proteinase inhibitor (trypsin) PDB id
3cti

 

 

 

 

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Contents
Protein chain
29 a.a.
PDB id:
3cti
Name: Proteinase inhibitor (trypsin)
Title: Relaxation matrix refinement of the solution structure of squash trypsin inhibitor
Structure: Trypsin inhibitor. Chain: a. Engineered: yes
Source: Cucurbita maxima. Winter squash. Organism_taxid: 3661
NMR struc: 6 models
Authors: M.Nilges,J.Habazettl,A.T.Bruenger,T.A.Holak
Key ref: M.Nilges et al. (1991). Relaxation matrix refinement of the solution structure of squash trypsin inhibitor. J Mol Biol, 219, 499-510. PubMed id: 2051485
Date:
27-Mar-91     Release date:   15-Apr-92    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01074  (ITR1_CUCMA) -  Trypsin inhibitor 1 from Cucurbita maxima
Seq:
Struc: 		29 a.a.
29 a.a.
Key:    PfamA domain  Secondary structure

 

 
J Mol Biol 219:499-510 (1991)
PubMed id: 2051485  
 
 
Relaxation matrix refinement of the solution structure of squash trypsin inhibitor.
M.Nilges, J.Habazettl, A.T.Brünger, T.A.Holak.
 
  ABSTRACT  
 
The structure of the small squash trypsin inhibitor CMTI-I is refined by directly minimizing the difference between the observed two-dimensional nuclear Overhauser enhancement (NOE) intensities and those calculated by the full relaxation matrix approach. To achieve this, a term proportional to this difference was added to the potential energy function of the molecular dynamics program X-PLOR. Derivatives with respect to atomic co-ordinates are calculated analytically. Spin diffusion effects are thus accounted for fully during the refinement. Initial structures for the refinement were those determined recently by solution nuclear magnetic resonance using the isolated two-spin approximation to derive distance range estimates. The fits to the nuclear magnetic resonance data improve significantly with only small shifts in the refined structures during a few cycles of conjugate gradient minimization. However, larger changes (approximately 1 A) in the conformation occur during simulated annealing, which is accompanied by a further reduction of the difference between experimental and calculated two-dimensional NOE intensities. The refined structures are closer to the X-ray structure of the inhibitor complexed with trypsin than the initial structures. The root-mean-square difference for backbone atoms between the initial structures and the X-ray structure is 0.96 A, and that between the refined structures and the X-ray structure 0.61 A.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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PDB codes: 2kyo 2kyp
20152154 V.Kuryavyi, and D.J.Patel (2010).
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PDB code: 2kpr
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PDB codes: 1kb1 1kbm
14556622 L.Jouvensal, L.Quillien, E.Ferrasson, Y.Rahbé, J.Guéguen, and F.Vovelle (2003).
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PDB code: 1p8b
12401802 L.Somerville, E.Y.Krynetski, N.F.Krynetskaia, R.D.Beger, W.Zhang, C.A.Marhefka, W.E.Evans, and R.W.Kriwacki (2003).
Structure and dynamics of thioguanine-modified duplex DNA.
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PDB codes: 1n14 1n17
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Atomic resolution structure of squash trypsin inhibitor: unexpected metal coordination.
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PDB code: 1lu0
10828944 D.G.Norman, R.J.Grainger, D.Uhrín, and D.M.Lilley (2000).
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PDB code: 1by6
10684926 S.T.Hsu, M.T.Chou, and J.W.Cheng (2000).
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10425682 A.Kettani, S.Bouaziz, E.Skripkin, A.Majumdar, W.Wang, R.A.Jones, and D.J.Patel (1999).
Interlocked mismatch-aligned arrowhead DNA motifs.
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PDB code: 1b3p
10090283 J.Badger, R.A.Kumar, P.Yip, and S.Szalma (1999).
New features and enhancements in the X-PLOR computer program.
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9876123 J.P.Rife, S.C.Stallings, C.C.Correll, A.Dallas, T.A.Steitz, and P.B.Moore (1999).
Comparison of the crystal and solution structures of two RNA oligonucleotides.
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9649303 A.Gelasco, and S.J.Lippard (1998).
NMR solution structure of a DNA dodecamer duplex containing a cis-diammineplatinum(II) d(GpG) intrastrand cross-link, the major adduct of the anticancer drug cisplatin.
  Biochemistry, 37, 9230-9239.
PDB code: 1a84
9600889 G.M.Clore, and A.M.Gronenborn (1998).
New methods of structure refinement for macromolecular structure determination by NMR.
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9145109 A.Kettani, S.Bouaziz, W.Wang, R.A.Jones, and D.J.Patel (1997).
Bombyx mori single repeat telomeric DNA sequence forms a G-quadruplex capped by base triads.
  Nat Struct Biol, 4, 382-389.
PDB code: 1aff
9100003 C.W.Cross, J.S.Rice, and X.Gao (1997).
Solution structure of an RNA x DNA hybrid duplex containing a 3'-thioformacetal linker and an RNA A-tract.
  Biochemistry, 36, 4096-4107.
PDB code: 1ac3
9305987 D.Cullinan, F.Johnson, A.P.Grollman, M.Eisenberg, and C.de los Santos (1997).
Solution structure of a DNA duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite 2'-deoxyguanosine.
  Biochemistry, 36, 11933-11943.
PDB code: 1b6x
9154915 M.Foti, S.Marshalko, E.Schurter, S.Kumar, G.P.Beardsley, and B.I.Schweitzer (1997).
Solution structure of a DNA decamer containing the antiviral drug ganciclovir: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement.
  Biochemistry, 36, 5336-5345.
PDB code: 1ac9
9219245 M.G.Hinds, and R.S.Norton (1997).
NMR spectroscopy of peptides and proteins. Practical considerations.
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9054564 T.Nishizaki, S.Iwai, E.Ohtsuka, and H.Nakamura (1997).
Solution structure of an RNA.2'-O-methylated RNA hybrid duplex containing an RNA.DNA hybrid segment at the center.
  Biochemistry, 36, 2577-2585.
PDB code: 1nao
8873597 A.Korobka, D.Cullinan, M.Cosman, A.P.Grollman, D.J.Patel, M.Eisenberg, and C.de los Santos (1996).
Solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite 2'-deoxyadenosine, determined by NMR spectroscopy and restrained molecular dynamics.
  Biochemistry, 35, 13310-13318.
PDB code: 1b6y
8873598 D.Cullinan, A.Korobka, A.P.Grollman, D.J.Patel, M.Eisenberg, and C.de los Santos (1996).
NMR solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite thymidine: comparison with the duplex containing deoxyadenosine opposite the adduct.
  Biochemistry, 35, 13319-13327.
PDB code: 1b5k
8740365 J.Ji, M.E.Hogan, and X.Gao (1996).
Solution structure of an antiparallel purine motif triplex containing a T.CG pyrimidine base triple.
  Structure, 4, 425-435.  
8913683 M.Nilges (1996).
Structure calculation from NMR data.
  Curr Opin Struct Biol, 6, 617-623.  
8672435 T.Nishizaki, S.Iwai, T.Ohkubo, C.Kojima, H.Nakamura, Y.Kyogoku, and E.Ohtsuka (1996).
Solution Strucutres of DNA duplexes containing a DNA x RNA hybrid region, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) and d(GGAGA)r(UGAC) x d(GTCATCTCC).
  Biochemistry, 35, 4016-4025.
PDB codes: 1dhh 1drn
  8575189 A.M.Gronenborn, and G.M.Clore (1995).
Structures of protein complexes by multidimensional heteronuclear magnetic resonance spectroscopy.
  Crit Rev Biochem Mol Biol, 30, 351-385.  
7894084 R.T.Clowes, A.Crawford, A.R.Raine, B.O.Smith, and E.D.Laue (1995).
Improved methods for structural studies of proteins using nuclear magnetic resonance spectroscopy.
  Curr Opin Biotechnol, 6, 81-88.  
8075980 I.Radhakrishnan, and D.J.Patel (1994).
Solution structure of a pyrimidine.purine.pyrimidine DNA triplex containing T.AT, C+.GC and G.TA triples.
  Structure, 2, 17-32.
PDB code: 149d
  8003965 K.J.Nielsen, D.Alewood, J.Andrews, S.B.Kent, and D.J.Craik (1994).
An 1H NMR determination of the three-dimensional structures of mirror-image forms of a Leu-5 variant of the trypsin inhibitor from Ecballium elaterium (EETI-II).
  Protein Sci, 3, 291-302.
PDB code: 2let
  7849598 P.K.Pallaghy, K.J.Nielsen, D.J.Craik, and R.S.Norton (1994).
A common structural motif incorporating a cystine knot and a triple-stranded beta-sheet in toxic and inhibitory polypeptides.
  Protein Sci, 3, 1833-1839.  
7892175 P.Koehl, and M.Delarue (1994).
Polar and nonpolar atomic environments in the protein core: implications for folding and binding.
  Proteins, 20, 264-278.  
8460109 A.M.Bonvin, J.A.Rullmann, R.M.Lamerichs, R.Boelens, and R.Kaptein (1993).
"Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applied to the solution structure of crambin.
  Proteins, 15, 385-400.
PDB code: 1ccm
8210313 A.T.Brünger, and M.Nilges (1993).
Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR-spectroscopy.
  Q Rev Biophys, 26, 49.  
8069626 I.Radhakrishnan, and D.J.Patel (1993).
Solution structure of a purine.purine.pyrimidine DNA triplex containing G.GC and T.AT triples.
  Structure, 1, 135-152.
PDB codes: 134d 135d 136d
  8318898 M.J.Sutcliffe (1993).
Representing an ensemble of NMR-derived protein structures by a single structure.
  Protein Sci, 2, 936-944.  
8081740 Y.Wang, and D.J.Patel (1993).
Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex.
  Structure, 1, 263-282.
PDB code: 143d
1549601 Q.X.Hua, M.Kochoyan, and M.A.Weiss (1992).
Structure and dynamics of des-pentapeptide-insulin in solution: the molten-globule hypothesis.
  Proc Natl Acad Sci U S A, 89, 2379-2383.
PDB code: 1his
1368432 W.J.Chazin (1992).
NMR structures and methodology.
  Curr Opin Biotechnol, 3, 326-332.  
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 codes are shown on the right.

 

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