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- PDB-5lvz: Crystal structure of yeast 14-3-3 protein from Lachancea thermoto... -

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Basic information

Entry
Database: PDB / ID: 5lvz
TitleCrystal structure of yeast 14-3-3 protein from Lachancea thermotolerans
ComponentsKLTH0G14146p
KeywordsSIGNALING PROTEIN / 14-3-3
Function / homology
Function and homology information


14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein ...14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesLachancea thermotolerans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKlima, M. / Boura, E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal structures of a yeast 14-3-3 protein from Lachancea thermotolerans in the unliganded form and bound to a human lipid kinase PI4KB-derived peptide reveal high evolutionary conservation.
Authors: Eisenreichova, A. / Klima, M. / Boura, E.
History
DepositionSep 14, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionOct 19, 2016ID: 5LHO
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: KLTH0G14146p


Theoretical massNumber of molelcules
Total (without water)28,6041
Polymers28,6041
Non-polymers00
Water1,62190
1
A: KLTH0G14146p

A: KLTH0G14146p


Theoretical massNumber of molelcules
Total (without water)57,2082
Polymers57,2082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2030 Å2
ΔGint-9 kcal/mol
Surface area23000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.120, 122.780, 39.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein KLTH0G14146p


Mass: 28603.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284) (fungus)
Gene: KLTH0G14146g / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: C5DN49
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.7 Å3/Da / Density % sol: 54.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 13% PEG 3350, 190 mM CaCl2, 3% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.95→44.34 Å / Num. obs: 23282 / % possible obs: 99.91 % / Redundancy: 8.4 % / Biso Wilson estimate: 36.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09166 / Rsym value: 0.09166 / Net I/σ(I): 14.26
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.323 / Mean I/σ(I) obs: 1.48 / CC1/2: 0.617 / % possible all: 99.96

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Processing

Software
NameVersionClassification
XDSversion Oct 15, 2015 BUILT=20151231data reduction
XDSversion Oct 15, 2015 BUILT=20151231data scaling
PHASERversion 2.5.6phasing
PHENIXversion 1.9-1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A4O

1a4o


Resolution: 1.95→44.34 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.5
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 1163 5 %random selection
Rwork0.1892 ---
obs0.1909 23276 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.5 Å2
Refinement stepCycle: LAST / Resolution: 1.95→44.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1869 0 0 90 1959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121899
X-RAY DIFFRACTIONf_angle_d1.2112564
X-RAY DIFFRACTIONf_dihedral_angle_d13.757715
X-RAY DIFFRACTIONf_chiral_restr0.05292
X-RAY DIFFRACTIONf_plane_restr0.006327
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection Rfree: 5 % / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.95-2.03880.28471420.27232689
2.0388-2.14620.2591430.23382729
2.1462-2.28070.24411430.2152714
2.2807-2.45680.27651450.22152745
2.4568-2.7040.21861430.21112724
2.704-3.09520.24481460.20412760
3.0952-3.89930.20831460.17232817
3.8993-44.340.19871550.16382935

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