[English] 日本語
Yorodumi
- PDB-1dnk: THE X-RAY STRUCTURE OF THE DNASE I-D(GGTATACC)2 COMPLEX AT 2.3 AN... -

+
Open data


ID or keywords:

Loading...

-
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 (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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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 (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 / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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
2EDTAEthylenediaminetetraacetic acid11
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more