[English] 日本語
Yorodumi
- PDB-2dnj: DNASE I-INDUCED DNA CONFORMATION. 2 ANGSTROMS STRUCTURE OF A DNAS... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2dnj
TitleDNASE I-INDUCED DNA CONFORMATION. 2 ANGSTROMS STRUCTURE OF A DNASE I-OCTAMER COMPLEX
Components
  • 5'-D(*GP*CP*GP*AP*TP*C)-3'
  • 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'
  • DEOXYRIBONUCLEASE I
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 Å
AuthorsLahm, A. / Suck, D.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: DNase I-induced DNA conformation. 2 A structure of a DNase I-octamer complex
Authors: Lahm, A. / Suck, D.
#1: 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.
#2: 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.
#3: 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.
#4: Journal: J.Mol.Biol. / Year: 1982
Title: Crystallization and Preliminary Crystallographic Data of Bovine Pancreatic Deoxyribonuclease I
Authors: Suck, D.
#5: 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
DepositionOct 21, 1986Deposition 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: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Category: struct_conf / struct_conf_type
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_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 2.0Oct 21, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_conn
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_chem_comp_identifier.comp_id / _pdbx_chem_comp_identifier.identifier / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'
C: 5'-D(*GP*CP*GP*AP*TP*C)-3'
A: DEOXYRIBONUCLEASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5514
Polymers33,3293
Non-polymers2211
Water4,540252
1
B: 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'
C: 5'-D(*GP*CP*GP*AP*TP*C)-3'
A: DEOXYRIBONUCLEASE I
hetero molecules

B: 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'
C: 5'-D(*GP*CP*GP*AP*TP*C)-3'
A: DEOXYRIBONUCLEASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1018
Polymers66,6596
Non-polymers4422
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)72.900, 100.100, 92.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
DetailsTHE ASYMMETRIC UNIT CONTAINS ONE DNASE I MOLECULE AND ONE NICKED DNA OCTAMER WITH A TOTAL OF 14 NUICLEOTIDES. THE CLEAVED 3-PRIME GC OF ONE OF THE DNA STRANDS IS MISSING IN THE STRUCTURE. THE SYMMETRY OPERATION X,1-Y,1-Z, I.E. THE TWOFOLD AXIS ALONG A AT B/2,C/2, CREATES THE QUASI-CONTINUOUS 14-MER FORMED BY THE TWO OVERLAPPING NICKE OCTAMERS.

-
Components

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


Mass: 2427.605 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*CP*GP*AP*TP*C)-3'


Mass: 1809.218 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DEOXYRIBONUCLEASE I / / EC 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, deoxyribonuclease I
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsOF THE CARBOHYDRATE MOIETY ATTACHED TO ND2 ASN 18, ONLY THE FIRST RESIDUE WAS VISIBLE IN THE ...OF THE CARBOHYDRATE MOIETY ATTACHED TO ND2 ASN 18, ONLY THE FIRST RESIDUE WAS VISIBLE IN THE ELECTRON DENSITY MAP AND IS INCLUDED IN THE ENTRY.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 600011
3EDT11
4IMIDAZOLE11
5NACLSodium chloride11
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-ID
115 mMEDTA1
28 %(w/v)PEG60001
31
41
51

-
Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE
DetectorDetector: OSCILLATION CAMERA
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 20921 / Observed criterion σ(F): 3
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / % possible obs: 89.2 % / Rmerge(I) obs: 0.076

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→6 Å / σ(F): 0 /
RfactorNum. reflection% reflection
obs0.174 20101 90.2 %
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 281 14 252 2553
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0310.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0290.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.51.5
X-RAY DIFFRACTIONp_mcangle_it2.32.25
X-RAY DIFFRACTIONp_scbond_it3.42.5
X-RAY DIFFRACTIONp_scangle_it54
X-RAY DIFFRACTIONp_plane_restr0.0180.02
X-RAY DIFFRACTIONp_chiral_restr0.1840.15
X-RAY DIFFRACTIONp_singtor_nbd0.160.2
X-RAY DIFFRACTIONp_multtor_nbd0.230.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.20.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.23
X-RAY DIFFRACTIONp_staggered_tor15.815
X-RAY DIFFRACTIONp_orthonormal_tor34.130
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: 20101 / σ(F): 0 / Rfactor all: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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