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- PDB-4npu: Crystal Structure of HIV-1 Protease Multiple Mutant P51 -

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Basic information

Entry
Database: PDB / ID: 4npu
TitleCrystal Structure of HIV-1 Protease Multiple Mutant P51
ComponentsProtease
KeywordsHYDROLASE / HIV-1 protease / P51 / multiple mutant / drug resistance
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: 1.5 Å
AuthorsZhang, Y. / Weber, I.T.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Structures of darunavir-resistant HIV-1 protease mutant reveal atypical binding of darunavir to wide open flaps.
Authors: Zhang, Y. / Chang, Y.C. / Louis, J.M. / Wang, Y.F. / Harrison, R.W. / Weber, I.T.
History
DepositionNov 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease
B: Protease


Theoretical massNumber of molelcules
Total (without water)21,5692
Polymers21,5692
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-17 kcal/mol
Surface area10500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.685, 46.685, 101.617
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Protease


Mass: 10784.627 Da / Num. of mol.: 2
Mutation: Q7K, D25N, V32I, L33F, N37S, V54M, C67A, A82I, I84V, C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O38896
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M imidazole, 1.0 M sodium acetate trihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2012
RadiationMonochromator: SI220 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 34414 / Num. obs: 34414 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 23.2
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 4.6 / Num. unique all: 3310 / % possible all: 95.5

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3UF3

3uf3


Resolution: 1.5→23.64 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.347 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19744 1735 5 %RANDOM
Rwork0.15891 ---
obs0.1609 32677 99.39 %-
all-34414 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.633 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.5→23.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 0 134 1654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191596
X-RAY DIFFRACTIONr_bond_other_d0.0020.021631
X-RAY DIFFRACTIONr_angle_refined_deg2.071.9722176
X-RAY DIFFRACTIONr_angle_other_deg1.02833749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5335207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.61423.7761
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.115287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2411512
X-RAY DIFFRACTIONr_chiral_restr0.1490.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211798
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02350
X-RAY DIFFRACTIONr_rigid_bond_restr8.47133227
X-RAY DIFFRACTIONr_sphericity_free19.698557
X-RAY DIFFRACTIONr_sphericity_bonded9.02753267
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 96 -
Rwork0.163 2281 -
obs--94.18 %

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