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- PDB-3vgz: Crystal structure of E. coli YncE -

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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
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 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

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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

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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

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