[English] 日本語
Yorodumi
- PDB-1d2i: CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE BGLII COMPLEXED WIT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1d2i
TitleCRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE BGLII COMPLEXED WITH DNA 16-MER
Components
  • DNA (5'-D(*TP*AP*TP*TP*AP*TP*AP*GP*AP*TP*CP*TP*AP*TP*AP*A)-3')
  • PROTEIN (RESTRICTION ENDONUCLEASE BGLII)
KeywordsHYDROLASE/DNA / RESTRICTION ENDONUCLEASE / RESTRICTION ENZYME / PROTEIN-DNA COMPLEX / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / magnesium ion binding / DNA binding
Similarity search - Function
Restriction endonuclease, type II, BamHI/BglIII/BstY / Restriction Endonuclease - #20 / Restriction Endonuclease / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Type II restriction enzyme BglII
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsLukacs, C.M. / Kucera, R. / Schildkraut, I. / Aggarwal, A.K.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution.
Authors: Lukacs, C.M. / Kucera, R. / Schildkraut, I. / Aggarwal, A.K.
History
DepositionSep 23, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: DNA (5'-D(*TP*AP*TP*TP*AP*TP*AP*GP*AP*TP*CP*TP*AP*TP*AP*A)-3')
D: DNA (5'-D(*TP*AP*TP*TP*AP*TP*AP*GP*AP*TP*CP*TP*AP*TP*AP*A)-3')
A: PROTEIN (RESTRICTION ENDONUCLEASE BGLII)
B: PROTEIN (RESTRICTION ENDONUCLEASE BGLII)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9036
Polymers61,8544
Non-polymers492
Water9,782543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.800, 101.700, 116.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 4895.228 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: OLIGOMERS WERE PRODUCED COMMERCIALLY
#2: Protein PROTEIN (RESTRICTION ENDONUCLEASE BGLII)


Mass: 26031.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: Q45488
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.2
Details: 15- 20% PEG 4000, 0.2 M AMMONIUM SULFATE, 0.1 M MES PH 5.2, MICROBATCH, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18-10 mg/mlprotein11
217-20 %PEG154011
30.2 Mammonium sulfate11
40.1 MMES11

-
Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9494, 0.9791, 0.9792
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 28, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.94941
20.97911
30.97921
ReflectionResolution: 1.7→99 Å / Num. all: 123664 / Num. obs: 123664 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13
Reflection shellResolution: 1.7→1.78 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.162 / % possible all: 99.3
Reflection
*PLUS
Num. measured all: 629080 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 99.3 %

-
Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.7→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
Details: NUMBERS IN REFLECTION DETAILS SECTION REPRESENT DATA INCLUDING ANOMALOUS PAIRS. NUMBERS IN REFINEMENT SECTION DO NOT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2148 -RANDOM
Rwork0.182 ---
obs0.182 64782 99.9 %-
all-64782 --
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3590 650 2 543 4785
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0181
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.884
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 62634
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.88

+
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