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- PDB-4n5a: Crystal structure of Efr3 -

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Basic information

Entry
Database: PDB / ID: 4n5a
TitleCrystal structure of Efr3
ComponentsProtein EFR3
KeywordsPROTEIN BINDING / HEAT-like repeats / component of Stt4 complex / Ypp1 / Plasma membrane
Function / homologyProtein EFR3 / : / EFR3 protein / cell periphery / protein localization to plasma membrane / mitochondrion / plasma membrane / Protein EFR3
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.204 Å
AuthorsWu, X. / Chi, R.J. / Baskin, J.M. / Lucast, L. / Burd, C.G. / De Camilli, P. / Reinisch, K.M.
CitationJournal: Dev.Cell / Year: 2014
Title: Structural insights into assembly and regulation of the plasma membrane phosphatidylinositol 4-kinase complex.
Authors: Wu, X. / Chi, R.J. / Baskin, J.M. / Lucast, L. / Burd, C.G. / De Camilli, P. / Reinisch, K.M.
History
DepositionOct 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Oct 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein EFR3


Theoretical massNumber of molelcules
Total (without water)64,7821
Polymers64,7821
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.374, 136.374, 141.143
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Protein EFR3


Mass: 64781.941 Da / Num. of mol.: 1 / Fragment: residues 8-562
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: EFR3, YMR212C, YM8261.06C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03653
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: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.35ul each of protein solution and mother liquor (0.08M sodium cacodylate, 0.16 M calcium acetate, 11.5% PEG 8000, 20% glycerol) and 0.3ul of 0.1 M EDTA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→29.53 Å / Num. obs: 13197 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 14.3 %
Reflection shellResolution: 3.2→3.31 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHARPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.204→29.526 Å / SU ML: 0.39 / σ(F): 2.08 / Phase error: 28.89 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2556 661 5.01 %RANDOM
Rwork0.2311 ---
obs0.2324 12535 99.58 %-
all-13197 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.204→29.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4326 0 0 0 4326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044395
X-RAY DIFFRACTIONf_angle_d0.7385936
X-RAY DIFFRACTIONf_dihedral_angle_d11.8951655
X-RAY DIFFRACTIONf_chiral_restr0.051702
X-RAY DIFFRACTIONf_plane_restr0.003744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2035-3.45050.37171290.31042447X-RAY DIFFRACTION100
3.4505-3.79710.31971300.26922454X-RAY DIFFRACTION100
3.7971-4.34510.27011300.23462469X-RAY DIFFRACTION100
4.3451-5.46860.22371330.22182517X-RAY DIFFRACTION99
5.4686-29.52710.23071390.20932648X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5371.4060.9837.11181.15951.2105-0.10180.0847-0.1673-0.49470.0715-0.1914-0.07070.15990.07450.58170.05340.07720.43480.02290.2131-11.981147.4309134.0186
22.5205-1.7637-1.48556.58780.98920.5492-0.0466-0.10160.91390.57510.10450.6529-0.2048-0.0235-0.09420.81430.0767-0.09590.5442-0.0151.0909-23.203791.4529143.1978
34.6644-0.7372-0.73416.89180.53913.8593-0.27050.2057-0.6934-0.35180.0018-0.36270.5097-0.02720.35810.67260.02750.05350.4869-0.17240.6784-46.135127.4897154.9267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 9:207)
2X-RAY DIFFRACTION2(chain A and resid 208:444)
3X-RAY DIFFRACTION3(chain A and resid 445:560)

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