3DNI

CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF DNASE I AT 2 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.177 

wwPDB Validation 3D Report Full Report



Literature

Crystallographic refinement and structure of DNase I at 2 A resolution.

Oefner, C.Suck, D.

(1986) J Mol Biol 192: 605-632

  • DOI: 10.1016/0022-2836(86)90280-9
  • Primary Citation of Related Structures:  
    3DNI

  • PubMed Abstract: 
  • The structure of bovine pancreatic deoxyribonuclease I (DNase I) has been refined at 2 A resolution using the restrained parameter, reciprocal least-squares procedure of Hendrickson and Konnert. The conventional R-factor for 16,104 reflections with I ...

    The structure of bovine pancreatic deoxyribonuclease I (DNase I) has been refined at 2 A resolution using the restrained parameter, reciprocal least-squares procedure of Hendrickson and Konnert. The conventional R-factor for 16,104 reflections with I greater than or equal to 3 sigma (I) from 6.0 to 2.0 A resolution is 0.157. Bond lengths and angles of the refined structure are close to ideal values with root-mean-square (r.m.s.) deviations of 0.023 A and 1.4 degrees, respectively. The r.m.s. deviation of short non-bonded contacts from the sum of van der Waals' radii is 0.18 A. The orientation of side-chains shows a clear trimodal distribution of chi 1-angles at -60 degrees, 180 degrees, 60 degrees (in the order of preference) corresponding to staggered conformations. The chemically determined sequence was corrected at four positions, the major correction being an insertion of the tripeptide Ile-Val-Arg between Arg27 and Arg28. Extended hydrophobic regions in between, and on either side of, the two central six-stranded beta-pleated sheets are mainly responsible for the low average isotropic temperature factor of 11.9 A2 for the 2033 protein atoms. Besides the flexible loop region between Gly97 and Gly102 (Glu99 and Ser100 are disordered) and the carbohydrate side-chain, which both extend into a large solvent channel, only the exposed loop Arg70 to Lys74 shows elevated thermal mobility. The longest of the eight helices in DNase I, together representing 26% of the structure, has a 22 degree kink and consists of two alpha-helical segments (residues 136 to 144 and 145 to 155) separated by a 3(10)-helical turn. DNase I fragments 1 to 120 and 121 to 257 can be superimposed by an approximate 2-fold axis (r.m.s. deviation 1.49 A for 61 equivalent C alpha positions), suggesting that the enzyme might be the result of gene duplication. The two Ca2+ bound to DNase I under crystallization conditions are important for its structural integrity by stabilizing the surface loop Asp198 to Thr204 and limiting the region of high thermal mobility in the flexible loop to residues Gly97 to Gly102. The N-linked carbohydrate side-chain attached to Asn18 is of the high-mannose type with a branching point at the mannose residue in position 3.(ABSTRACT TRUNCATED AT 400 WORDS)


    Related Citations: 
    • X-Ray Structure of the DNase I-D(Ggtatacc)2 Complex at 2.3 Angstroms Resolution
      Weston, S.A., Lahm, A., Suck, D.
      (1992) J Mol Biol 226: 1237
    • DNase I-Induced DNA Conformation. 2 Angstroms Structure of a DNase I-Octamer Complex
      Lahm, A., Suck, D.
      (1991) J Mol Biol 221: 645
    • Structure Refined to 2 Angstroms of a Nicked DNA Octanucleotide Complex with DNase I
      Suck, D., Lahm, A., Oefner, C.
      (1988) Nature 332: 465
    • Structure of DNase I at 2.0 Angstroms Resolution Suggests a Mechanism for Binding to and Cutting DNA
      Suck, D., Oefner, C.
      (1986) Nature 321: 620
    • Three-Dimensional Structure of Bovine Pancreatic DNase I at 2.5 Angstroms Resolution
      Suck, D., Oefner, C., Kabsch, W.
      (1984) EMBO J 3: 2423
    • Crystallization and Preliminary Crystallographic Data of Bovine Pancreatic Deoxyribonuclease I
      Suck, D.
      (1982) J Mol Biol 162: 511
    • Bovine Pancreatic Deoxyribonucleasea. Isolation of Cyanogen Bromide Peptides, Complete Covalent Structure of the Polypeptide Chain
      Liao, T.-H., Salnikow, J., Moore, S., Stein, W.H.
      (1973) J Biol Chem 248: 1489

    Organizational Affiliation

    CEINGE Biotecnologie Avanzate scarlm, Via G. Salvatore, Napoli, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DEOXYRIBONUCLEASE IA260Bos taurusMutation(s): 0 
Gene Names: DNASE1DNL1
EC: 3.1.21.1
Find proteins for P00639 (Bos taurus)
Explore P00639 
Go to UniProtKB:  P00639
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-galactopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
7 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.6α = 90
b = 54.9β = 91.4
c = 38.4γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1992-08-20 
  • Released Date: 1994-01-31 
  • Deposition Author(s): Oefner, C., Suck, D.

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary