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- PDB-3dni: CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF DNASE I AT 2 ANGSTRO... -

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Basic information

Entry
Database: PDB / ID: 3dni
TitleCRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF DNASE I AT 2 ANGSTROMS RESOLUTION
ComponentsDEOXYRIBONUCLEASE I
KeywordsENDONUCLEASE
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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsOefner, C. / Suck, D.
Citation
Journal: J.Mol.Biol. / Year: 1986
Title: Crystallographic refinement and structure of DNase I at 2 A resolution.
Authors: Oefner, C. / Suck, D.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: X-Ray Structure of the DNase I-D(Ggtatacc)2 Complex at 2.3 Angstroms Resolution
Authors: Weston, S.A. / Lahm, A. / Suck, D.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: DNase I-Induced DNA Conformation. 2 Angstroms Structure of a DNase I-Octamer Complex
Authors: Lahm, A. / Suck, D.
#3: 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.
#4: 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.
#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 Deoxyribonucleasea. 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 20, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
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_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _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 / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEOXYRIBONUCLEASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4084
Polymers29,0931
Non-polymers1,3153
Water6,756375
1
A: DEOXYRIBONUCLEASE I
hetero molecules

A: DEOXYRIBONUCLEASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8168
Polymers58,1852
Non-polymers2,6316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y,-z+11
Unit cell
Length a, b, c (Å)131.600, 54.900, 38.400
Angle α, β, γ (deg.)90.00, 91.40, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: OF THE CARBOHYDRATE MOIETY ATTACHED TO ASN 18, 7 RESIDUES HAVE BEEN REFINED AND INCLUDED IN THE ENTRY. THE CARBOHYDRATE MOIETY IS ARRANGED AS FOLLOWS: MAN (264) - MAN (265) / N18 - NAG(261) - ...1: OF THE CARBOHYDRATE MOIETY ATTACHED TO ASN 18, 7 RESIDUES HAVE BEEN REFINED AND INCLUDED IN THE ENTRY. THE CARBOHYDRATE MOIETY IS ARRANGED AS FOLLOWS: MAN (264) - MAN (265) / N18 - NAG(261) - NAG(262) - MAN(263) \ MAN (266) - MAN (267) WHERE MAN (263) - MAN (264) IS LINKED 1-6 MAN (263) - MAN (266) IS LINKED 1-4

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Components

#1: Protein DEOXYRIBONUCLEASE I


Mass: 29092.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: pancreas / References: UniProt: P00639, deoxyribonuclease I
#2: Polysaccharide alpha-D-galactopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)-alpha-D- ...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


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-6DManpb1-3[DManpb1-6DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a2112h-1a_1-5][a1122h-1a_1-5]/1-1-2-2-3-4-2/a4-b1_b4-c1_c3-d1_c6-f1_d6-e1_f6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(6+1)][a-D-Galp]{}}[(6+1)][a-D-Altp]{[(6+1)][b-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 6.6 / Method: unknown / Details: referred to J.Mol.Biol. 162.511-513 1982
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
111 %PEG600012
270 mMimidazole12
3100 mM12NaCl
40.1 mM12CaCl2
50.1 mM12NaN3
63.5 mg/mlprotein11
7enzyme12

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.5 Å / Num. obs: 9025 / % possible obs: 86 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.064

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→6 Å / σ(F): 0 /
RfactorNum. reflection
obs0.177 17774
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 85 375 2494
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0230.02
X-RAY DIFFRACTIONp_angle_d0.030.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.030.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.161
X-RAY DIFFRACTIONp_mcangle_it1.911.5
X-RAY DIFFRACTIONp_scbond_it1.511
X-RAY DIFFRACTIONp_scangle_it2.341.5
X-RAY DIFFRACTIONp_plane_restr0.0190.02
X-RAY DIFFRACTIONp_chiral_restr0.1430.1
X-RAY DIFFRACTIONp_singtor_nbd0.1830.3
X-RAY DIFFRACTIONp_multtor_nbd0.1770.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2130.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.12
X-RAY DIFFRACTIONp_staggered_tor19.715
X-RAY DIFFRACTIONp_orthonormal_tor34.220
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. reflection all: 17774 / σ(F): 0 / Rfactor all: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS

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