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- PDB-3o40: Complex of a chimeric alpha/beta-peptide based on the gp41 CHR do... -

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Basic information

Entry
Database: PDB / ID: 3o40
TitleComplex of a chimeric alpha/beta-peptide based on the gp41 CHR domain bound to gp41-5
Components
  • chimeric alpha/beta peptide based on gp41 CHR domain sequence
  • gp41-5
KeywordsVIRAL PROTEIN / HIV fusion inhibitor / mixed alpha-peptide/beta-peptide backbone
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHorne, W.S. / Johnson, L.M. / Gellman, S.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Broad Distribution of Energetically Important Contacts across an Extended Protein Interface.
Authors: Johnson, L.M. / Horne, W.S. / Gellman, S.H.
History
DepositionJul 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Structure summary
Revision 1.2Sep 6, 2023Group: 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 / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: gp41-5
B: chimeric alpha/beta peptide based on gp41 CHR domain sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4647
Polymers26,7382
Non-polymers7265
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-27 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.846, 56.968, 103.466
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein gp41-5


Mass: 22246.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide chimeric alpha/beta peptide based on gp41 CHR domain sequence


Mass: 4491.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide

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Non-polymers , 4 types, 65 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M MgCl2, 0.1 M Tris pH 8.5, 30% w/v PEG 4000 , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 9, 2009
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 16963 / % possible obs: 99.7 % / Redundancy: 6.2 % / Rsym value: 0.108 / Net I/σ(I): 15.6

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Processing

Software
NameVersionClassification
MD2diffractometer softwaredata collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3O3X

3o3x


Resolution: 2.1→25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.395 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21206 859 5.1 %RANDOM
Rwork0.17057 ---
obs0.17264 16063 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.903 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å20 Å2
2---0.45 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 34 60 1951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211986
X-RAY DIFFRACTIONr_bond_other_d0.0050.021358
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.9642683
X-RAY DIFFRACTIONr_angle_other_deg0.95633336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1165237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31426.132106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19815358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7061512
X-RAY DIFFRACTIONr_chiral_restr0.0880.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0192193
X-RAY DIFFRACTIONr_gen_planes_other0.0010.019356
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_it1.6761.51181
X-RAY DIFFRACTIONr_mcbond_other0.5061.5505
X-RAY DIFFRACTIONr_mcangle_it3.03521883
X-RAY DIFFRACTIONr_scbond_it4.6463805
X-RAY DIFFRACTIONr_scangle_it7.5334.5791
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.104→2.158 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 64 -
Rwork0.158 1105 -
obs--95.58 %

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