[English] 日本語
Yorodumi
- PDB-3vh0: Crystal structure of E. coli YncE complexed with DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vh0
TitleCrystal structure of E. coli YncE complexed with DNA
Components
  • DNA (5'-D(*CP*GP*GP*GP*TP*AP*CP*TP*CP*AP*G)-3')
  • Uncharacterized protein YncE
KeywordsPROTEIN BINDING/DNA / beta-propeller / PROTEIN BINDING-DNA complex
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / DNA binding
Similarity search - Function
: / YNCE-like beta-propeller / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Uncharacterized protein YncE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKagawa, W. / Sagawa, T. / Niki, H. / Kurumizaka, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structural basis for the DNA-binding activity of the bacterial beta-propeller protein YncE
Authors: Kagawa, W. / Sagawa, T. / Niki, H. / Kurumizaka, H.
History
DepositionAug 23, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Sep 18, 2013Group: Derived calculations
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein YncE
B: Uncharacterized protein YncE
C: Uncharacterized protein YncE
D: Uncharacterized protein YncE
E: DNA (5'-D(*CP*GP*GP*GP*TP*AP*CP*TP*CP*AP*G)-3')
F: DNA (5'-D(*CP*GP*GP*GP*TP*AP*CP*TP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)161,4086
Polymers161,4086
Non-polymers00
Water54030
1
A: Uncharacterized protein YncE
D: Uncharacterized protein YncE
E: DNA (5'-D(*CP*GP*GP*GP*TP*AP*CP*TP*CP*AP*G)-3')
F: DNA (5'-D(*CP*GP*GP*GP*TP*AP*CP*TP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)84,0784
Polymers84,0784
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein YncE


Theoretical massNumber of molelcules
Total (without water)38,6651
Polymers38,6651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Uncharacterized protein YncE


Theoretical massNumber of molelcules
Total (without water)38,6651
Polymers38,6651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.172, 171.172, 177.215
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

-
Components

#1: Protein
Uncharacterized protein YncE


Mass: 38664.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yncE / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76116
#2: DNA chain DNA (5'-D(*CP*GP*GP*GP*TP*AP*CP*TP*CP*AP*G)-3')


Mass: 3374.210 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The DNA contains a short self-annealing sequence, GTAC.
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 4.02 Å3/Da / Density % sol: 69.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: tri-sodium citrate, tacsimate, PEG 3350, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 7, 2009
RadiationMonochromator: Rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 56609 / Num. obs: 56581 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rsym value: 0.064 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
2.9-37.86.356370.3771100
3-3.127.89.356310.2561100
3.12-3.277.812.856240.181100
3.27-3.447.819.556470.1151100
3.44-3.657.824.156780.0871100
3.65-3.947.83056250.0671100
3.94-4.337.839.356650.0511100
4.33-4.967.851.456380.0411100
4.96-6.247.838.657040.0581100
6.24-507.656.257320.041199.8

-
Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
CNS1.21refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VGZ

3vgz


Resolution: 2.9→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.234 2867 RANDOM
Rwork0.21 --
obs0.21 56353 -
all-56391 -
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9910 448 0 30 10388
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d0.737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
2.9-30.3253000.3043X-RAY DIFFRACTION531010
3-3.120.33092810.3082X-RAY DIFFRACTION532410
3.12-3.270.30462690.2878X-RAY DIFFRACTION533010
3.27-3.440.3022800.2677X-RAY DIFFRACTION534410
3.44-3.650.26762730.2349X-RAY DIFFRACTION538310
3.65-3.940.24912970.216X-RAY DIFFRACTION531010
3.94-4.330.21582740.195X-RAY DIFFRACTION536010
4.33-4.960.16272950.1467X-RAY DIFFRACTION534510
4.96-6.240.21553100.1927X-RAY DIFFRACTION536210
6.24-500.20782880.1835X-RAY DIFFRACTION541810

+
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