3DNI

CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF DNASE I AT 2 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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

Oefner, C.Suck, D.

(1986) J.Mol.Biol. 192: 605-632


  • 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: 
    • Crystallization and Preliminary Crystallographic Data of Bovine Pancreatic Deoxyribonuclease I
      Suck, D.
      (1982) J.Mol.Biol. 162: 511
    • DNase I-Induced DNA Conformation. 2 Angstroms Structure of a DNase I-Octamer Complex
      Lahm, A.,Suck, D.
      (1991) J.Mol.Biol. 221: 645
    • 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
    • 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
    • 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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DEOXYRIBONUCLEASE I
A
260Bos taurusMutation(s): 0 
Gene Names: DNASE1 (DNL1)
EC: 3.1.21.1
Find proteins for P00639 (Bos taurus)
Go to Gene View: DNASE1
Go to UniProtKB:  P00639
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GLA
Query on GLA

Download SDF File 
Download CCD File 
A
ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 131.600α = 90.00
b = 54.900β = 91.40
c = 38.400γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other