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- PDB-5b18: Crystal Structure of a Darunavir Resistant HIV-1 Protease -

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Basic information

Entry
Database: PDB / ID: 5b18
TitleCrystal Structure of a Darunavir Resistant HIV-1 Protease
ComponentsProtease
KeywordsHYDROLASE / HIV-1 protease / drug resistance / darunavir / flap
Function / homology
Function and homology information


retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination ...retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / DNA binding / zinc ion binding
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / 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. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Exoribonuclease H
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSuzuki, K. / Ode, H. / Nakashima, M. / Sugiura, W. / Watanabe, N. / Suzuki, A. / Iwatani, Y.
CitationJournal: Front Microbiol / Year: 2016
Title: Unique Flap Conformation in an HIV-1 Protease with High-Level Darunavir Resistance
Authors: Nakashima, M. / Ode, H. / Suzuki, K. / Fujino, M. / Maejima, M. / Kimura, Y. / Masaoka, T. / Hattori, J. / Matsuda, M. / Hachiya, A. / Yokomaku, Y. / Suzuki, A. / Watanabe, N. / Sugiura, W. / Iwatani, Y.
History
DepositionNov 30, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
C: Protease
D: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,02010
Polymers43,7604
Non-polymers2606
Water2,612145
1
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0456
Polymers21,8802
Non-polymers1654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-30 kcal/mol
Surface area10190 Å2
MethodPISA
2
C: Protease
D: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9744
Polymers21,8802
Non-polymers942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-34 kcal/mol
Surface area10140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.149, 48.699, 54.151
Angle α, β, γ (deg.)89.900, 73.980, 86.690
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Protease


Mass: 10939.907 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: pET41a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: E5RVX9*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: LiCl, Na citrate, PEG 6000, Glycerol, Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 32575 / % possible obs: 96 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.046 / Χ2: 2.4 / Net I/av σ(I): 26.936 / Net I/σ(I): 17 / Num. measured all: 62603
Reflection shell

Diffraction-ID: 1 / Redundancy: 1.9 % / Rejects: _

Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.860.23331661.45192.7
1.86-1.940.16632301.6395.2
1.94-2.030.11932381.92895.9
2.03-2.130.09632332.10296.2
2.13-2.270.07932852.40696.1
2.27-2.440.07132802.59496.5
2.44-2.690.05532772.62497
2.69-3.080.04632963.15997.2
3.08-3.880.03832933.14497.1
3.88-500.03232772.90596.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KJ7

1kj7


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.088 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 1646 5.1 %RANDOM
Rwork0.1925 ---
obs0.1951 30928 95.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.29 Å2 / Biso mean: 27.055 Å2 / Biso min: 11.63 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å20.11 Å2-0.83 Å2
2---1.08 Å2-0.36 Å2
3----0.99 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 0 12 145 3229
Biso mean--34.66 34.05 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193227
X-RAY DIFFRACTIONr_angle_refined_deg2.0161.9824390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.55418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.68824.262122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20615599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0881521
X-RAY DIFFRACTIONr_chiral_restr0.1380.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212361
LS refinement shellResolution: 1.796→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 110 -
Rwork0.27 2113 -
all-2223 -
obs--88.74 %

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