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- PDB-4r0r: Ebolavirus GP Prehairpin Intermediate Mimic -

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Basic information

Entry
Database: PDB / ID: 4r0r
TitleEbolavirus GP Prehairpin Intermediate Mimic
ComponentseboIZN21
KeywordsBIOSYNTHETIC PROTEIN / coiled-coil / N-trimer / prehairpin intermediate
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsClinton, T.R. / Weinstock, M.T. / Jacobsen, M.T. / Szabo-Fresnais, N. / Pandya, M.J. / Whitby, F.G. / Herbert, A.S. / Prugar, L.I. / McKinnon, R. / Hill, C.P. ...Clinton, T.R. / Weinstock, M.T. / Jacobsen, M.T. / Szabo-Fresnais, N. / Pandya, M.J. / Whitby, F.G. / Herbert, A.S. / Prugar, L.I. / McKinnon, R. / Hill, C.P. / Welch, B.D. / Dye, J.M. / Eckert, D.M. / Kay, M.S.
CitationJournal: Protein Sci. / Year: 2015
Title: Design and characterization of ebolavirus GP prehairpin intermediate mimics as drug targets.
Authors: Clinton, T.R. / Weinstock, M.T. / Jacobsen, M.T. / Szabo-Fresnais, N. / Pandya, M.J. / Whitby, F.G. / Herbert, A.S. / Prugar, L.I. / McKinnon, R. / Hill, C.P. / Welch, B.D. / Dye, J.M. / Eckert, D.M. / Kay, M.S.
History
DepositionAug 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: eboIZN21


Theoretical massNumber of molelcules
Total (without water)5,6221
Polymers5,6221
Non-polymers00
Water1086
1
A: eboIZN21

A: eboIZN21

A: eboIZN21


Theoretical massNumber of molelcules
Total (without water)16,8653
Polymers16,8653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area5000 Å2
ΔGint-49 kcal/mol
Surface area9980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.510, 38.510, 72.588
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-604-

HOH

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Components

#1: Protein/peptide eboIZN21


Mass: 5621.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Synthetic peptide (protein) eboIZN21 dissolved in ddH2O at 10 mg/ml mixed in 2:1 protein:well buffer ratio with 30% (v/v) 1,2-propanediol, 100 mM HEPES pH 7.5, 20% (v/v) PEG-400 at 4 degrees ...Details: Synthetic peptide (protein) eboIZN21 dissolved in ddH2O at 10 mg/ml mixed in 2:1 protein:well buffer ratio with 30% (v/v) 1,2-propanediol, 100 mM HEPES pH 7.5, 20% (v/v) PEG-400 at 4 degrees Celcius (277 K), VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2014
RadiationMonochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 3680 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 25.6 % / Biso Wilson estimate: 47.66 Å2 / Rmerge(I) obs: 0.054 / Χ2: 1.091 / Net I/σ(I): 16.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.2314.90.9143471.172199.7
2.23-2.3216.50.7893421.51199.7
2.32-2.4219.70.4153701.157199.7
2.42-2.55230.4043581.031100
2.55-2.7123.40.2593561.0941100
2.71-2.9224.10.1633641.0381100
2.92-3.21250.113731.0541100
3.21-3.6827.70.0773660.9551100
3.68-4.6337.30.0493811.051100
4.63-4040.50.0364231.0961100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.14data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CANONICAL HELICAL MODEL OF IZN AND N-TRIMER MODEL

Resolution: 2.15→19.585 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 42.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2937 355 9.76 %random
Rwork0.2724 ---
obs0.2742 3636 98.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.59 Å2 / Biso mean: 69.015 Å2 / Biso min: 40.63 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms396 0 0 6 402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002397
X-RAY DIFFRACTIONf_angle_d0.503528
X-RAY DIFFRACTIONf_chiral_restr0.02162
X-RAY DIFFRACTIONf_plane_restr0.00166
X-RAY DIFFRACTIONf_dihedral_angle_d15.524163
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.4610.43191130.31551066117999
2.461-3.09870.32131120.304510861198100
3.0987-19.5850.26631300.25591129125997

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