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- PDB-2erl: PHEROMONE ER-1 FROM -

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Basic information

Entry
Database: PDB / ID: 2erl
TitlePHEROMONE ER-1 FROM
ComponentsMATING PHEROMONE ER-1
KeywordsPHEROMONE
Function / homology
Function and homology information


pheromone activity / extracellular region / plasma membrane
Similarity search - Function
Pheromone ER-1 / Pheromone Er-1, protozoan / Protozoan pheromone superfamily / Pheromone, protozoan / Euplotes raikovi mating pheromone / Pheromone ER-1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ETHANOL / Mating pheromone Er-1/Er-3
Similarity search - Component
Biological speciesEuplotes raikovi (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 1 Å
AuthorsAnderson, D.H. / Weiss, M.S. / Eisenberg, D.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: A challenging case for protein crystal structure determination: the mating pheromone Er-1 from Euplotes raikovi.
Authors: Anderson, D.H. / Weiss, M.S. / Eisenberg, D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: A Cooperative Model for Receptor Recognition and Cell Adhesion: Evidence from the Molecular Packing in the 1.6-A Crystal Structure of the Pheromone Er-1 from the Ciliated Protozoan Euplotes Raikovi
Authors: Weiss, M.S. / Anderson, D.H. / Raffioni, S. / Bradshaw, R.A. / Ortenzi, C. / Luporini, P. / Eisenberg, D.
#2: Journal: Protein Sci. / Year: 1994
Title: The NMR Solution Structure of the Pheromone Er-1 from the Ciliated Protozoan Euplotes Raikovi
Authors: Mronga, S. / Luginbuhl, P. / Brown, L.R. / Ortenzi, C. / Luporini, P. / Bradshaw, R.A. / Wuthrich, K.
#3: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallization of the Euplotes Raikovi Mating Pheromone Er-1
Authors: Anderson, D. / Raffioni, S. / Luporini, P. / Bradshaw, R.A. / Eisenberg, D.
#4: Journal: J.Biol.Chem. / Year: 1988
Title: Primary Structure of the Mating Pheromone Er-1 of the Ciliate Euplotes Raikovi
Authors: Raffioni, S. / Luporini, P. / Chait, B.T. / Disper, S.S. / Bradshaw, R.A.
History
DepositionDec 20, 1995Processing site: BNL
SupersessionJul 11, 1996ID: 1ERL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MATING PHEROMONE ER-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4642
Polymers4,4181
Non-polymers461
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.910, 23.100, 23.100
Angle α, β, γ (deg.)90.00, 110.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide MATING PHEROMONE ER-1


Mass: 4417.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euplotes raikovi (eukaryote) / References: UniProt: P10774
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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

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Sample preparation

CrystalDensity Matthews: 1.53 Å3/Da / Density % sol: 19.6 %
Crystal
*PLUS
Density % sol: 20 %
Crystal grow
*PLUS
Temperature: 298-301 K / pH: 3.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14.4 mg/mlEr-11drop
20.068 Mammonium sulfate1drop
30.028 Msodium citrate1drop
43.33 %(v/v)ethanol1droppH3.50
50.12-0.15 Mammonium sulfate1reservoir
60.05 Msodium citrate1reservoirpH3.50
76 %(v/v)ethanol1reservoir

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Data collection

Diffraction sourceWavelength: 0.7107
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 20, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7107 Å / Relative weight: 1
ReflectionResolution: 1→25.26 Å / Num. obs: 13659 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.054
Reflection
*PLUS
Lowest resolution: 8 Å / Num. obs: 13461 / % possible obs: 92.4 % / Num. measured all: 101188

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Processing

Software
NameClassification
MARRESEARCHdata collection
SHELXL-93model building
SHELXL-93refinement
MARdata reduction
SHELXL-93phasing
RefinementResolution: 1→25.25 Å / Num. parameters: 3121 / Num. restraintsaints: 3883 / σ(F): 0
Stereochemistry target values: ENGH AND HUBER (1991) ACTA CRYST. A47, 392-400
Details: ANISOTROPIC TEMPERATURE FACTORS HAVE BEEN REFINED FOR THE NON-HYDROGEN ATOMS IN THIS ENTRY. HYDROGEN ATOMS HAVE ISOTROPIC U'S THAT ARE 1.2 TIMES THE ISOTROPIC U'S OF THE ATOMS ON WHICH THEY ...Details: ANISOTROPIC TEMPERATURE FACTORS HAVE BEEN REFINED FOR THE NON-HYDROGEN ATOMS IN THIS ENTRY. HYDROGEN ATOMS HAVE ISOTROPIC U'S THAT ARE 1.2 TIMES THE ISOTROPIC U'S OF THE ATOMS ON WHICH THEY RIDE. THE QUANTITIES ON THE ANISOU RECORD FOR EACH HYDROGEN ATOM ARE THE EQUIVALENT-TO-ISOTROPIC U'S.
Rfactor% reflection
Rfree0.165 -
obs0.129 93.8 %
Solvent computationSolvent model: DRIESSEN, ET AL., (1989) J.APPL.CRYST. 22, 510-516
Refine analyzeNum. disordered residues: 4 / Occupancy sum non hydrogen: 1
Refinement stepCycle: LAST / Resolution: 1→25.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms319 0 3 20 342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.022
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.206
X-RAY DIFFRACTIONs_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.078
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.021
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.035
X-RAY DIFFRACTIONs_approx_iso_adps0.083
Software
*PLUS
Name: SHELXL / Version: 93 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.129 / Lowest resolution: 26 Å / % reflection Rfree: 10 % / Rfactor obs: 0.1292
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.206

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