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- PDB-1dnk: THE X-RAY STRUCTURE OF THE DNASE I-D(GGTATACC)2 COMPLEX AT 2.3 AN... -

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Basic information

Entry
Database: PDB / ID: 1dnk
TitleTHE X-RAY STRUCTURE OF THE DNASE I-D(GGTATACC)2 COMPLEX AT 2.3 ANGSTROMS RESOLUTION
Components
  • DNA (5'-D(*GP*GP*TP*AP*TP*AP*C)-3')
  • DNA (5'-D(*GP*GP*TP*AP*TP*AP*CP*C)-3')
  • PROTEIN (DEOXYRIBONUCLEASE I (DNASE I) (E.C.3.1.21.1))
KeywordsHYDROLASE/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / deoxyribonuclease I / deoxyribonuclease I activity / neutrophil activation involved in immune response / DNA catabolic process / nuclear envelope / actin binding / apoptotic process ...regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / deoxyribonuclease I / deoxyribonuclease I activity / neutrophil activation involved in immune response / DNA catabolic process / nuclear envelope / actin binding / apoptotic process / DNA binding / extracellular region / nucleus
Similarity search - Function
Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family ...Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / Deoxyribonuclease-1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsWeston, S.A. / Lahm, A. / Suck, D.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 A resolution.
Authors: Weston, S.A. / Lahm, A. / Suck, D.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: DNAse I induced DNA conformation: 2 Angstroms structure of a DNAse-octamer complex
Authors: Lahm, A. / Suck, D.
#2: Journal: Nature / Year: 1988
Title: Structure refined to 2 Angstroms of a nicked DNA octanucleotide complex with DNAse I
Authors: Suck, D. / Lahm, A. / Oefner, C.
#3: Journal: Nature / Year: 1986
Title: Structure of DNase I at 2.0 Angstroms resolution suggests a mechanism for binding to and cutting DNA
Authors: Suck, D. / Oefner, C.
#4: Journal: J.Mol.Biol. / Year: 1986
Title: Crystallographic refinement and structure of DNAse I at 2 Angstroms resolution
Authors: Oefner, C. / Suck, D.
#5: Journal: Embo J. / Year: 1984
Title: Three-dimensional structure of bovine pancreatic DNAse I at 2.5 Angstroms resolution
Authors: Suck, D. / Oefner, C. / Kabsch, W.
#6: Journal: J.Mol.Biol. / Year: 1982
Title: Crystallization and preliminary crystallographic data of bovine pancreatic deoxyribonuclease I
Authors: Suck, D.
#7: Journal: J.Biol.Chem. / Year: 1973
Title: Bovine pancreatic deoxyribonuclease A. Isolation of cyanogen bromide peptides, complete covalent structure of the polypeptide chain
Authors: Liao, T.-H. / Salnikow, J. / Moore, S. / Stein, W.H.
History
DepositionAug 10, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*GP*GP*TP*AP*TP*AP*C)-3')
C: DNA (5'-D(*GP*GP*TP*AP*TP*AP*CP*C)-3')
A: PROTEIN (DEOXYRIBONUCLEASE I (DNASE I) (E.C.3.1.21.1))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0814
Polymers33,6573
Non-polymers4241
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.100, 108.400, 62.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: OF THE CARBOHYDRATE MOIETY ATTACHED TO ND2 ASN 18, ONLY THE FIRST TWO RESIDUES WERE VISIBLE IN THE ELECTRON DENSITY MAP.

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Components

#1: DNA chain DNA (5'-D(*GP*GP*TP*AP*TP*AP*C)-3')


Mass: 2137.435 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*GP*TP*AP*TP*AP*CP*C)-3')


Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (DEOXYRIBONUCLEASE I (DNASE I) (E.C.3.1.21.1))


Mass: 29092.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / Secretion: MILK / References: UniProt: P00639
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsOF THE CARBOHYDRATE MOIETY ATTACHED TO ND2 ASN 18, ONLY THE FIRST TWO RESIDUES WERE VISIBLE IN THE ...OF THE CARBOHYDRATE MOIETY ATTACHED TO ND2 ASN 18, ONLY THE FIRST TWO RESIDUES WERE VISIBLE IN THE ELECTRON DENSITY MAP.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2EDTA11
3WATER12
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1protein1drop
2DNA1drop
30.3 M1dropNaCl
420 mMEDTA1drop
550-60 %satsodium citrate1drop
60.3 M1reservoirNaCl
720 mMEDTA1reservoir
850-60 %satsodium citrate1reservoir

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Data collection

DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→18.89 Å / Num. obs: 12681 / Observed criterion σ(F): 3 / Rmerge(I) obs: 0.076

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Processing

Software
NameClassification
TNTrefinement
PROLSQrefinement
RefinementResolution: 2.3→6 Å / σ(F): 0 /
RfactorNum. reflection
obs0.188 11998
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 303 28 77 2390
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 6 Å / Num. reflection all: 11998 / σ(F): 0 / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONt_bond_d0.0160.02
X-RAY DIFFRACTIONt_angle_d0.0390.03
X-RAY DIFFRACTIONt_planar_d0.0390.04
X-RAY DIFFRACTIONt_plane_restr0.0140.02
X-RAY DIFFRACTIONt_chiral_restr0.1680.15
X-RAY DIFFRACTIONt_mcbond_it1.41.5
X-RAY DIFFRACTIONt_scbond_it4.022.5
X-RAY DIFFRACTIONt_mcangle_it2.32.25
X-RAY DIFFRACTIONt_scangle_it5.054.5

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