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- PDB-3oqa: Crystal Structures of Multidrug-Resistant Clinical Isolate 769 HI... -

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Entry
Database: PDB / ID: 3oqa
TitleCrystal Structures of Multidrug-Resistant Clinical Isolate 769 HIV-1 Protease Variants
ComponentsHIV-1 Protease
KeywordsHYDROLASE / Protease
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / endonuclease activity / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
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. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Cathepsin D, subunit A; domain 1 / Acid Proteases / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Gag-Pol polyprotein / Pol protein
Similarity search - Component
Biological speciesHuman Immunodeficiency Virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsYedidi, R.S. / Proteasa, G. / Martinez-Cajas, J.L. / Vickrey, J.F. / Martin, P.D. / Wawrzak, Z. / Kovari, L.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Contribution of the 80s loop of HIV-1 protease to the multidrug-resistance mechanism: crystallographic study of MDR769 HIV-1 protease variants.
Authors: Yedidi, R.S. / Proteasa, G. / Martinez, J.L. / Vickrey, J.F. / Martin, P.D. / Wawrzak, Z. / Liu, Z. / Kovari, I.A. / Kovari, L.C.
History
DepositionSep 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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: HIV-1 Protease


Theoretical massNumber of molelcules
Total (without water)10,7561
Polymers10,7561
Non-polymers00
Water99155
1
A: HIV-1 Protease

A: HIV-1 Protease


Theoretical massNumber of molelcules
Total (without water)21,5112
Polymers21,5112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area2950 Å2
ΔGint-18 kcal/mol
Surface area10630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.136, 45.136, 102.709
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein HIV-1 Protease


Mass: 10755.608 Da / Num. of mol.: 1 / Fragment: UNP residues 1-99 / Mutation: T82S
Source method: isolated from a genetically manipulated source
Details: Multidrug-resistant clinical isolate # 769 HIV-1 protease
Source: (gene. exp.) Human Immunodeficiency Virus 1 / Strain: MDR769 / Gene: pol / Plasmid: pRSET B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q000H7, UniProt: P35963*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.3-1.0M sodium chloride in the pH range 5.5-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 22, 2004 / Details: HighRes2 mirror system
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→27.28 Å / Num. obs: 5466 / Redundancy: 6.4 % / Rsym value: 0.071
Reflection shellHighest resolution: 2.25 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 764 / Rsym value: 0.371

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TW7

1tw7


Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.845 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23778 243 4.5 %RANDOM
Rwork0.20228 ---
obs0.20396 5196 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.434 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms755 0 0 55 810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022769
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.9761045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.9232528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79315136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.717154
X-RAY DIFFRACTIONr_chiral_restr0.0990.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02556
X-RAY DIFFRACTIONr_nbd_refined0.2220.2284
X-RAY DIFFRACTIONr_nbtor_refined0.320.2509
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.214
X-RAY DIFFRACTIONr_mcbond_it1.371.5499
X-RAY DIFFRACTIONr_mcangle_it1.8672797
X-RAY DIFFRACTIONr_scbond_it2.6083295
X-RAY DIFFRACTIONr_scangle_it4.4094.5248
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 17 -
Rwork0.271 357 -
obs--99.2 %

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