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- PDB-3vh0: Crystal structure of E. coli YncE complexed with DNA -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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