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- PDB-2g69: Structure of Unliganded HIV-1 Protease F53L Mutant -

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Basic information

Entry
Database: PDB / ID: 2g69
TitleStructure of Unliganded HIV-1 Protease F53L Mutant
Componentsprotease
KeywordsHYDROLASE / aspartic protease / catalysis / unliganded / flap mutant / non-active site mutant
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 / symbiont-mediated suppression of host gene expression / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / identical protein 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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 / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsKovalevsky, A.Y. / Liu, F.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Mechanism of Drug Resistance Revealed by the Crystal Structure of the Unliganded HIV-1 Protease with F53L Mutation.
Authors: Liu, F. / Kovalevsky, A.Y. / Louis, J.M. / Boross, P.I. / Wang, Y.F. / Harrison, R.W. / Weber, I.T.
History
DepositionFeb 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protease


Theoretical massNumber of molelcules
Total (without water)10,7071
Polymers10,7071
Non-polymers00
Water1,63991
1
A: protease

A: protease


Theoretical massNumber of molelcules
Total (without water)21,4132
Polymers21,4132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2900 Å2
ΔGint-13 kcal/mol
Surface area10040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.946, 60.946, 55.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1050-

HOH

DetailsThe asymmetric unit contains HIV-1 protease monomer. The active dimer is constructed by rotation around the crystallographic 2 fold axis of the P4(1)2(1)2 space group.

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Components

#1: Protein protease


Mass: 10706.660 Da / Num. of mol.: 1 / Fragment: HIV-1 protease monomer / Mutation: Q7K, L33I, F53L, L63I, C67A, C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli)
References: UniProt: P03368, UniProt: Q7SSI0*PLUS, HIV-1 retropepsin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: The reservoir contained 0.2 M sodium citrate, phosphate buffer (pH = 6.0-6.4), 10% DMSO, and 20-30% saturated ammonium sulfate as a precipitant., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 12, 2003
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→10 Å / Num. all: 22779 / Num. obs: 19437 / % possible obs: 85.3 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2
Reflection shellResolution: 1.35→1.4 Å / % possible all: 97.3

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
MAR345data collection
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→10 Å / Num. parameters: 7676 / Num. restraintsaints: 8854 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1138 5 %RANDOM
Rwork0.1552 ---
obs0.1597 19437 --
all-22779 --
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 811 / Occupancy sum non hydrogen: 830.5
Refinement stepCycle: LAST / Resolution: 1.35→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms753 0 0 91 844
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0308
X-RAY DIFFRACTIONs_zero_chiral_vol0.057
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.072
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.069
X-RAY DIFFRACTIONs_approx_iso_adps0

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