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- PDB-6o54: Crystal Structure of multi-drug resistant HIV-1 protease PR-S17 (D25N) -

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Basic information

Entry
Database: PDB / ID: 6o54
TitleCrystal Structure of multi-drug resistant HIV-1 protease PR-S17 (D25N)
ComponentsHIV-1 protease
KeywordsHYDROLASE / Viral Protein / HIV PROTEASE
Function / homology
Function and homology information


host multivesicular body / aspartic-type endopeptidase activity / virion membrane / proteolysis
Similarity search - Function
Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsWang, Y.-F. / Brothers, R. / Agniswamy, J. / Weber, I.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM062920 United States
CitationJournal: Acs Omega / Year: 2019
Title: Highly Drug-Resistant HIV-1 Protease Mutant PRS17 Shows Enhanced Binding to Substrate Analogues.
Authors: Agniswamy, J. / Kneller, D.W. / Brothers, R. / Wang, Y.F. / Harrison, R.W. / Weber, I.T.
History
DepositionMar 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
X: HIV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9325
Polymers10,7911
Non-polymers1424
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.645, 49.645, 86.703
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11X-6-

TRP

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Components

#1: Protein HIV-1 protease


Mass: 10790.608 Da / Num. of mol.: 1 / Mutation: D25N, M46L, G48V, C67A, V77I, A82S, I93L, C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7BFC3
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.86 Å3/Da / Density % sol: 56.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.95 M sodium chloride, 0.1 M Bis-Tris, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.21→50 Å / Num. obs: 35459 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.035 / Net I/σ(I): 18.7
Reflection shellResolution: 1.21→1.25 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2 / Num. unique obs: 1956 / CC1/2: 0.751 / Rpim(I) all: 0.318 / Χ2: 1.004 / % possible all: 52.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-20000.98.712data scaling
PHASERphasing
SHELXL2014refinement
HKL-20000.98.712data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T2E

5t2e


Resolution: 1.21→38.55 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.06 / SU ML: 0.021 / Cross valid method: FREE R-VALUE / ESU R: 0.035 / ESU R Free: 0.034 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16411 1701 4.8 %Random
Rwork0.14776 ---
obs0.14854 33739 91.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å2-0 Å2
2---0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.21→38.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms761 0 4 105 870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.013836
X-RAY DIFFRACTIONr_bond_other_d0.0020.017851
X-RAY DIFFRACTIONr_angle_refined_deg2.0071.6421154
X-RAY DIFFRACTIONr_angle_other_deg1.4341.5691981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7045116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45122.536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.66915153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.584155
X-RAY DIFFRACTIONr_chiral_restr0.1210.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02927
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02160
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_it4.4321.795413
X-RAY DIFFRACTIONr_mcbond_other4.4371.793412
X-RAY DIFFRACTIONr_mcangle_it5.732.69519
X-RAY DIFFRACTIONr_mcangle_other5.7252.691520
X-RAY DIFFRACTIONr_scbond_it4.5562.191423
X-RAY DIFFRACTIONr_scbond_other4.5562.19423
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7683.126626
X-RAY DIFFRACTIONr_long_range_B_refined6.25321.402842
X-RAY DIFFRACTIONr_long_range_B_other6.20721.148835
X-RAY DIFFRACTIONr_rigid_bond_restr6.64731687
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.209→1.24 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 71 -
Rwork0.259 1257 -
obs--47.5 %

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