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- PDB-8ci7: Apo-crystal structure of a wild-type South African HIV-1 subtype ... -

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Basic information

Entry
Database: PDB / ID: 8ci7
TitleApo-crystal structure of a wild-type South African HIV-1 subtype C protease at 2.4 angstrom
ComponentsTruncated pol polyprotein
KeywordsHYDROLASE / AIDS / HIV / Protease / subtype C protease / South African
Function / homology
Function and homology information


viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / endonuclease activity / aspartic-type endopeptidase activity / proteolysis / DNA binding
Similarity search - Function
Reverse transcriptase thumb / Reverse transcriptase thumb domain / Retropepsin-like catalytic domain / 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 ...Reverse transcriptase thumb / Reverse transcriptase thumb domain / Retropepsin-like catalytic domain / 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 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Truncated pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDlamini, N.P. / Pandian, R. / Onisuru, O. / Achilonu, I.A. / Sayed, Y.
Funding support South Africa, United Kingdom, 2items
OrganizationGrant numberCountry
National Research Foundation in South AfricaNEP Grant No 129920 South Africa
Science and Technology Funding CouncilST/R002754/1 United Kingdom
CitationJournal: To Be Published
Title: Biophysical and biochemical characterization of a wild-type South African HIV-1 subtype C protease
Authors: Dlamini, N.P. / Pandian, R. / Onisuru, O. / Achilonu, I.A. / Sayed, Y.
History
DepositionFeb 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 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: Truncated pol polyprotein


Theoretical massNumber of molelcules
Total (without water)10,7671
Polymers10,7671
Non-polymers00
Water1,31573
1
A: Truncated pol polyprotein

A: Truncated pol polyprotein


Theoretical massNumber of molelcules
Total (without water)21,5342
Polymers21,5342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3010 Å2
ΔGint-17 kcal/mol
Surface area10590 Å2
Unit cell
Length a, b, c (Å)46.600, 46.600, 102.144
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-114-

HOH

21A-152-

HOH

31A-172-

HOH

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Components

#1: Protein Truncated pol polyprotein


Mass: 10766.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Escherichia coli pLysS / References: UniProt: Q994Q3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.37 Å3/Da / Density % sol: 48.1 % / Description: bipyramidal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5 mg/mL of wild-type South African HIV-1 subtype C protease in 10 mM of sodium acetate at pH 5 with the crystallization condition consisting of 0.1 M of bis-Tris at pH 6.5 and 3.0 M of NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS 3.0 MICROFOCUS / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Oct 26, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→22.39 Å / Num. obs: 4659 / % possible obs: 97.2 % / Redundancy: 4.5 % / Biso Wilson estimate: 36.62 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.106 / Rrim(I) all: 0.175 / Χ2: 0.98 / Net I/σ(I): 9.7
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 433 / CC1/2: 0.462

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→22.39 Å / SU ML: 0.3605 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.9822
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.221 241 5.18 %
Rwork0.2033 4408 -
obs0.2059 4649 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→22.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms755 0 0 75 830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026767
X-RAY DIFFRACTIONf_angle_d0.5631037
X-RAY DIFFRACTIONf_chiral_restr0.0486124
X-RAY DIFFRACTIONf_plane_restr0.0035129
X-RAY DIFFRACTIONf_dihedral_angle_d2.5913465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-3.020.34361170.27772103X-RAY DIFFRACTION95.12
3.02-22.390.22061240.17642305X-RAY DIFFRACTION97.63

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