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- PDB-3mgn: D-Peptide inhibitor PIE71 in complex with IQN17 -

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Basic information

Entry
Database: PDB / ID: 3mgn
TitleD-Peptide inhibitor PIE71 in complex with IQN17
Components
  • D-PEPTIDE INHIBITOR PIE71
  • IQN17
KeywordsVIRAL PROTEIN/VIRAL PROTEIN inhibitor / PIE71 / IQN17 / HIV / helix / coiled-coil / D-peptide inhibitor / VIRAL PROTEIN-VIRAL PROTEIN inhibitor complex
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / D-PEPTIDE INHIBITOR PIE71
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHill, C.P. / Whitby, F.G. / Kay, M. / Francis, N.
CitationJournal: J.Virol. / Year: 2010
Title: Design of a potent D-peptide HIV-1 entry inhibitor with a strong barrier to resistance.
Authors: Welch, B.D. / Francis, J.N. / Redman, J.S. / Paul, S. / Weinstock, M.T. / Reeves, J.D. / Lie, Y.S. / Whitby, F.G. / Eckert, D.M. / Hill, C.P. / Root, M.J. / Kay, M.S.
History
DepositionApr 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IQN17
B: IQN17
C: IQN17
D: IQN17
E: IQN17
F: IQN17
G: D-PEPTIDE INHIBITOR PIE71
H: D-PEPTIDE INHIBITOR PIE71
I: D-PEPTIDE INHIBITOR PIE71
J: D-PEPTIDE INHIBITOR PIE71
K: D-PEPTIDE INHIBITOR PIE71
L: D-PEPTIDE INHIBITOR PIE71


Theoretical massNumber of molelcules
Total (without water)44,04512
Polymers44,04512
Non-polymers00
Water7,008389
1
A: IQN17
B: IQN17
C: IQN17
H: D-PEPTIDE INHIBITOR PIE71
K: D-PEPTIDE INHIBITOR PIE71
L: D-PEPTIDE INHIBITOR PIE71


Theoretical massNumber of molelcules
Total (without water)22,0226
Polymers22,0226
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9650 Å2
ΔGint-80 kcal/mol
Surface area11330 Å2
MethodPISA
2
D: IQN17
E: IQN17
F: IQN17
G: D-PEPTIDE INHIBITOR PIE71
I: D-PEPTIDE INHIBITOR PIE71
J: D-PEPTIDE INHIBITOR PIE71


Theoretical massNumber of molelcules
Total (without water)22,0226
Polymers22,0226
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-85 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.920, 30.791, 132.802
Angle α, β, γ (deg.)90.000, 91.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
IQN17


Mass: 5466.574 Da / Num. of mol.: 6 / Source method: obtained synthetically
#2: Protein/peptide
D-PEPTIDE INHIBITOR PIE71


Type: Cyclic peptide / Class: Inhibitor / Mass: 1874.236 Da / Num. of mol.: 6 / Source method: obtained synthetically / References: D-PEPTIDE INHIBITOR PIE71
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: QIAGEN PACT condition G4 - 20% Peg 3350, 0.1 M Bis Tris Propane, pH 7.5, 0.2 M Potassium Thiocyanate, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 82774 / Num. obs: 82774 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.052 / Χ2: 0.954 / Net I/σ(I): 19.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.4-1.453.90.31681000.787197.6
1.45-1.513.90.15181340.995197.5
1.51-1.583.90.13681040.982196.9
1.58-1.6640.11980621.015196.6
1.66-1.764.40.10881011.052196.7
1.76-1.950.09282210.98197.7
1.9-2.0960.07483750.934199
2.09-2.397.40.06384170.9141100
2.39-3.027.50.04785210.8121100
3.02-3010.10.04887391.0551100

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Phasing

Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.95 Å
Translation2.5 Å27.95 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→27.94 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.313 / WRfactor Rwork: 0.286 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.789 / SU B: 1.349 / SU ML: 0.056 / SU R Cruickshank DPI: 0.084 / SU Rfree: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1654 2 %RANDOM
Rwork0.261 ---
obs0.262 82186 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.03 Å2 / Biso mean: 31.168 Å2 / Biso min: 6.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å2-0.08 Å2
2--0.43 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.4→27.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 0 389 3383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223097
X-RAY DIFFRACTIONr_angle_refined_deg1.0942.0344047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3465323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.90825.769104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25615602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7311519
X-RAY DIFFRACTIONr_chiral_restr0.0660.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212037
X-RAY DIFFRACTIONr_mcbond_it0.6621.51797
X-RAY DIFFRACTIONr_mcangle_it1.12522831
X-RAY DIFFRACTIONr_scbond_it1.70831300
X-RAY DIFFRACTIONr_scangle_it2.8224.51216
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 126 -
Rwork0.306 5818 -
all-5944 -
obs--97.71 %

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