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- PDB-1lv1: Crystal Structure Analysis of the non-active site mutant of tethe... -

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Basic information

Entry
Database: PDB / ID: 1lv1
TitleCrystal Structure Analysis of the non-active site mutant of tethered HIV-1 protease to 2.1A resolution
ComponentsHIV-1 protease
KeywordsHYDROLASE / beta-ribbon flap
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / peptidase activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / DNA binding / RNA binding / zinc ion binding / membrane / identical protein 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. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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 / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKumar, M. / Kannan, K.K. / Hosur, M.V. / Bhavesh, N.S. / Chatterjee, A. / Mittal, R. / Hosur, R.V.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2002
Title: Effects of remote mutation on the autolysis of HIV-1 PR: X-ray and NMR investigations.
Authors: Kumar, M. / Kannan, K.K. / Hosur, M.V. / Bhavesh, N.S. / Chatterjee, A. / Mittal, R. / Hosur, R.V.
History
DepositionMay 24, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 10, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 protease


Theoretical massNumber of molelcules
Total (without water)21,9031
Polymers21,9031
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.060, 63.060, 83.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein HIV-1 protease /


Mass: 21902.760 Da / Num. of mol.: 1 / Mutation: C95M/C1095A
Source method: isolated from a genetically manipulated source
Details: Tethered dimer linked by GGSSG / Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04585, HIV-1 retropepsin
#2: Water ChemComp-HOH / water / 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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 5% saturated ammonium sulfate, 200mM sodium phosphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
250 mMsodium acetate1drop
31 mMdithiothreitol1drop
45 %satammonium sulfate1reservoir
5200 mMsodium phosphate1reservoir
6100 mMsodium citrate1reservoirpH6.2

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200HB / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 2001 / Details: Totally reflecting MSC mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. all: 51200 / Num. obs: 11676 / % possible obs: 93.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.1
Reflection shellResolution: 2.1→2.2 Å / % possible all: 47
Reflection
*PLUS
Num. obs: 10245 / Num. measured all: 51200 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 85 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→14.75 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 319647.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 428 5.3 %RANDOM
Rwork0.194 ---
obs0.194 8047 73.3 %-
all-11676 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.9922 Å2 / ksol: 0.326686 e/Å3
Displacement parametersBiso mean: 39.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å26.1 Å20 Å2
2--0.95 Å20 Å2
3----1.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-8 Å
Luzzati sigma a0.36 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.1→14.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 0 55 1568
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.432
X-RAY DIFFRACTIONc_scbond_it2.32
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0.072 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.392 30 4.7 %
Rwork0.291 610 -
obs--47.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 15 Å / Num. reflection obs: 7619 / Rfactor obs: 0.1935 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.1935
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Rfactor Rfree: 0.392 / Rfactor Rwork: 0.2924 / Rfactor obs: 0.2924

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