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- PDB-4ej8: Apo HIV Protease (PR) dimer in closed form with fragment 1F1 in t... -

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Basic information

Entry
Database: PDB / ID: 4ej8
TitleApo HIV Protease (PR) dimer in closed form with fragment 1F1 in the outside/top of flap
ComponentsProtease
KeywordsHYDROLASE / apo protease / allostery / fragment binding / closed form
Function / homology
Function and homology information


: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA 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. / 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. / 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
1H-indole-6-carboxylic acid / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.347 Å
AuthorsTiefenbrunn, T. / Stout, C.D.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Small molecule regulation of protein conformation by binding in the Flap of HIV protease.
Authors: Tiefenbrunn, T. / Forli, S. / Baksh, M.M. / Chang, M.W. / Happer, M. / Lin, Y.C. / Perryman, A.L. / Rhee, J.K. / Torbett, B.E. / Olson, A.J. / Elder, J.H. / Finn, M.G. / Stout, C.D.
History
DepositionApr 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,33512
Polymers21,5352
Non-polymers80010
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-16 kcal/mol
Surface area10880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.947, 66.533, 91.713
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protease / / PR / Retropepsin


Mass: 10767.702 Da / Num. of mol.: 2 / Fragment: UNP residues 490-588 / Mutation: Q7K, L33I, L63I, C67A, C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: R8 / Gene: pol / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: P12499, HIV-1 retropepsin
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-1F1 / 1H-indole-6-carboxylic acid


Mass: 161.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7NO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M Tris, pH 7.5, 28% PEG4000, 10% DMSO, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Aug 4, 2010
RadiationMonochromator: multilayer mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.347→53.854 Å / Num. all: 7933 / Num. obs: 7885 / % possible obs: 99.4 % / Net I/σ(I): 8.14
Reflection shellResolution: 2.347→2.45 Å / Mean I/σ(I) obs: 1.93 / % possible all: 95.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 30.96 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.4 Å45.86 Å
Translation2.4 Å45.86 Å

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Processing

Software
NameVersionClassificationNB
SAINTV7.68Adata scaling
SCALAdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
PROTEUM PLUSPLUSdata collection
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.347→53.85 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.897 / WRfactor Rfree: 0.2032 / WRfactor Rwork: 0.1599 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8627 / SU B: 7.174 / SU ML: 0.174 / SU R Cruickshank DPI: 0.7086 / SU Rfree: 0.2761 / Cross valid method: THROUGHOUT / σ(F): 1.9 / ESU R: 0.709 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 361 4.6 %RANDOM
Rwork0.1899 ---
obs0.1923 7849 99.46 %-
all-7885 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 47.84 Å2 / Biso mean: 19.0359 Å2 / Biso min: 5.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.347→53.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 48 120 1684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191598
X-RAY DIFFRACTIONr_angle_refined_deg1.0752.0012156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.5682556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68715287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.703158
X-RAY DIFFRACTIONr_chiral_restr0.0630.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211138
LS refinement shellResolution: 2.347→2.408 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 14 -
Rwork0.192 476 -
all-490 -
obs--94.23 %

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