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- PDB-6e6n: Pheromone from Euplotes raikovi, Er-13 -

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Basic information

Entry
Database: PDB / ID: 6e6n
TitlePheromone from Euplotes raikovi, Er-13
ComponentsPheromone from Euplotes raikovi Er-13
KeywordsSIGNALING PROTEIN / PHEROMONE
Function / homologyPheromone, protozoan / Euplotes raikovi mating pheromone / Er-13 prepro-pheromone
Function and homology information
Biological speciesEuplotes raikovi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.363 Å
AuthorsFinke, A.D. / Marsh, M.E.
CitationJournal: To Be Published
Title: Ab initio crystal structure determination of Euplotes raikovi pheromones from high-resolution data
Authors: Finke, A.D. / Pedrini, B. / Alimenti, C. / Vallesi, A. / Luporini, P. / Marsh, M.
History
DepositionJul 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Pheromone from Euplotes raikovi Er-13


Theoretical massNumber of molelcules
Total (without water)4,0561
Polymers4,0561
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.116, 39.116, 19.446
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein/peptide Pheromone from Euplotes raikovi Er-13


Mass: 4056.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euplotes raikovi (eukaryote) / References: UniProt: A0A482LMF4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 1.83 Å3/Da / Density % sol: 32.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.1 M to 0.2 M (NH4)2SO4, 0.05 M Na Citrate pH 3.5 and 6% (v/v) ethanol, using 5-ul protein drops and 5 ul of reservoir solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.6198 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6198 Å / Relative weight: 1
ReflectionResolution: 1.36→39.12 Å / Num. obs: 85988 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 1 / Rmerge(I) obs: 0.0524 / Net I/σ(I): 9.41
Reflection shellResolution: 1.363→1.411 Å / Rmerge(I) obs: 0.8927 / CC1/2: 0.9315

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.363→39.12 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.256 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1803 648 10 %RANDOM
Rwork0.15218 ---
obs0.15506 5829 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 21.775 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2--0.6 Å20 Å2
3----1.2 Å2
Refinement stepCycle: 1 / Resolution: 1.363→39.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms276 0 0 23 299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02298
X-RAY DIFFRACTIONr_bond_other_d0.0040.02249
X-RAY DIFFRACTIONr_angle_refined_deg1.8461.935409
X-RAY DIFFRACTIONr_angle_other_deg1.0853583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.516541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg55.95128.57114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2151546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.243
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02358
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0258
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0761.012158
X-RAY DIFFRACTIONr_mcbond_other0.9481.003157
X-RAY DIFFRACTIONr_mcangle_it1.4981.511198
X-RAY DIFFRACTIONr_mcangle_other1.5361.518199
X-RAY DIFFRACTIONr_scbond_it2.2951.197140
X-RAY DIFFRACTIONr_scbond_other2.2881.189139
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1371.738210
X-RAY DIFFRACTIONr_long_range_B_refined5.8679.357380
X-RAY DIFFRACTIONr_long_range_B_other5.8329.011374
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.363→1.398 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 46 -
Rwork0.263 418 -
obs--99.57 %
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)
11.61550.0425-1.50454.5832-2.370311.80810.02020.0634-0.0498-0.39480.08610.19670.4109-0.0614-0.10630.0723-0.00360.00090.0989-0.01850.065111.9241.647-3.4
28.7273-0.8733-7.58354.31970.540410.35620.25980.50050.1134-0.0592-0.22050.0991-0.9303-0.2598-0.03940.1436-0.0161-0.00030.1115-0.01090.038413.6718.9440.417
38.81853.85023.73727.492.38025.40810.011-0.2246-0.02940.5796-0.0680.4423-0.1944-0.33420.05690.16370.00970.06580.1268-0.0080.10128.8074.6277.687
43.15350.07392.30725.0586-2.78046.38440.171-0.0382-0.2178-0.1237-0.07420.07070.1410.197-0.09690.0212-0.0132-0.00030.0863-0.0110.049714.089-2.3356.004
53.3725-1.6456-1.2715.7447-2.63885.06230.1079-0.1420.23960.333-0.1941-0.2937-0.62440.41960.08620.1506-0.1176-0.00990.1755-0.01990.101420.038.055.918
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 6
2X-RAY DIFFRACTION2A7 - 12
3X-RAY DIFFRACTION3A13 - 18
4X-RAY DIFFRACTION4A19 - 32
5X-RAY DIFFRACTION5A33 - 38

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