[English] 日本語
Yorodumi
- PDB-3vgz: Crystal structure of E. coli YncE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vgz
TitleCrystal structure of E. coli YncE
ComponentsUncharacterized protein YncE
KeywordsPROTEIN BINDING / beta-propeller
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
Uncharacterized protein YncE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 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

-
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


Theoretical massNumber of molelcules
Total (without water)155,4104
Polymers155,4104
Non-polymers00
Water5,675315
1
A: Uncharacterized protein YncE


Theoretical massNumber of molelcules
Total (without water)38,8521
Polymers38,8521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein YncE


Theoretical massNumber of molelcules
Total (without water)38,8521
Polymers38,8521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Uncharacterized protein YncE


Theoretical massNumber of molelcules
Total (without water)38,8521
Polymers38,8521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Uncharacterized protein YncE


Theoretical massNumber of molelcules
Total (without water)38,8521
Polymers38,8521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.170, 139.310, 173.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
Uncharacterized protein YncE


Mass: 38852.461 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): B834(DE3) / References: UniProt: P76116
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: sodium acetate, ammonium sulfate, PEG 4000, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97902, 0.97944, 1.00000
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2007
RadiationMonochromator: Fixed exit Si double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979021
20.979441
311
ReflectionResolution: 1.7→50 Å / Num. all: 157597 / Num. obs: 157493 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rsym value: 0.072 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.7-1.767.15.9155840.3271100
1.76-1.837.27.9156760.251100
1.83-1.917.211156170.181100
1.91-2.027.215.7156490.1241100
2.02-2.147.319.3156880.0991100
2.14-2.317.323.3157070.0791100
2.31-2.547.226.5157330.0681100
2.54-2.917.229.6158080.0671100
2.91-3.66733158740.0751100
3.66-506.543.7161570.048199.4

-
Processing

Software
NameVersionClassification
BSSdata collection
SHELXDphasing
CNS1.21refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.244 7587 RANDOM
Rwork0.22 --
obs0.22 150973 -
all-157798 -
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9906 0 0 315 10221
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d0.702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.7-1.760.29676920.2737X-RAY DIFFRACTION1273510
1.76-1.830.30097090.2596X-RAY DIFFRACTION1321310
1.83-1.910.26957160.2384X-RAY DIFFRACTION1360310
1.91-2.020.2577300.2207X-RAY DIFFRACTION1431810
2.02-2.140.25277610.2272X-RAY DIFFRACTION1471910
2.14-2.310.24567900.2213X-RAY DIFFRACTION1467210
2.31-2.540.25177830.2294X-RAY DIFFRACTION1480010
2.54-2.910.25538250.2374X-RAY DIFFRACTION1486110
2.91-3.660.24868000.2274X-RAY DIFFRACTION1505910
3.66-500.21077810.1904X-RAY DIFFRACTION1540610

+
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