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- PDB-3u71: Crystal Structure Analysis of South African wild type HIV-1 Subty... -

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Basic information

Entry
Database: PDB / ID: 3u71
TitleCrystal Structure Analysis of South African wild type HIV-1 Subtype C Protease
ComponentsHIV-1 Protease
KeywordsHYDROLASE / Beta sheet / apo / protease / South African / non-B subtype / viral polyprotein
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 / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Truncated pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.72 Å
AuthorsNaicker, P. / Fanucchi, S. / Achilonu, I.A. / Fernandes, M.A. / Dirr, H.W. / Sayed, Y.
CitationJournal: To be Published
Title: Crystal structure analysis of South African wild type HIV-1 subtype C apo protease
Authors: Naicker, P. / Fanucchi, S. / Achilonu, I.A. / Fernandes, M.A. / Dirr, H.W. / Sayed, Y.
History
DepositionOct 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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)10,7671
Polymers10,7671
Non-polymers00
Water00
1
A: HIV-1 Protease

A: HIV-1 Protease


Theoretical massNumber of molelcules
Total (without water)21,5342
Polymers21,5342
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3020 Å2
ΔGint-19 kcal/mol
Surface area10510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.928, 45.928, 99.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein HIV-1 Protease


Mass: 10766.799 Da / Num. of mol.: 1 / Fragment: UNP residues 1-99 / Mutation: Q7K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pET-11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q994Q3

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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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2 M sodium citrate tribasic dihydrate, 20% w/v PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Oct 5, 2009 / Details: Mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 8.18 % / Av σ(I) over netI: 91.2 / Number: 46145 / Rsym value: 0.2 / D res high: 2.697 Å / Num. obs: 5638 / % possible obs: 98.76
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRsym value
2.72.7910.413
2.792.9110.333
2.913.0410.306
3.043.210.292
3.23.410.276
3.43.6610.291
3.664.0310.26
4.034.6110.186
4.615.8110.148
ReflectionResolution: 2.697→49.98 Å / Num. obs: 3193 / % possible obs: 98.76 % / Redundancy: 8.18 % / Rsym value: 0.2 / Net I/σ(I): 91.204
Reflection shell
Resolution (Å)Highest resolution (Å)Rsym valueDiffraction-ID
2.697-2.7940.4131
2.794-2.9060.3331
2.906-3.0380.3061
3.038-3.1980.2921
3.198-3.3980.2761
3.398-3.6610.2911
3.661-4.0290.261
4.029-4.6120.1861
4.612-5.8090.1481
5.8090.1481

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.72 Å41.74 Å
Translation2.72 Å41.74 Å

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Processing

Software
NameVersionClassificationNB
SAINTV7.68Adata scaling
SAINTV7.68Adata reduction
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R8N

2r8n


Resolution: 2.72→41.73 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.86 / WRfactor Rfree: 0.2448 / WRfactor Rwork: 0.2035 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7822 / SU B: 36.15 / SU ML: 0.313 / SU R Cruickshank DPI: 2.7395 / SU Rfree: 0.3877 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.388 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2826 137 4.3 %RANDOM
Rwork0.2167 ---
obs0.2195 3193 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 48.23 Å2 / Biso mean: 25.7907 Å2 / Biso min: 11.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.72→41.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms755 0 0 0 755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022767
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.9981037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.389598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.8925.625
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03915147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.506153
X-RAY DIFFRACTIONr_chiral_restr0.110.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021541
X-RAY DIFFRACTIONr_mcbond_it0.6411.5488
X-RAY DIFFRACTIONr_mcangle_it1.2232793
X-RAY DIFFRACTIONr_scbond_it1.7023279
X-RAY DIFFRACTIONr_scangle_it2.8994.5244
LS refinement shellResolution: 2.72→2.791 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 9 -
Rwork0.35 208 -
all-217 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -2.6229 Å / Origin y: -4.5867 Å / Origin z: -11.2942 Å
111213212223313233
T0.0218 Å20.0143 Å2-0.0066 Å2-0.0761 Å2-0.016 Å2--0.0419 Å2
L0.4157 °20.4203 °20.2807 °2-0.4314 °20.263 °2--2.5586 °2
S-0.0378 Å °0.1505 Å °-0.0464 Å °-0.0112 Å °0.1308 Å °-0.0616 Å °-0.0731 Å °-0.0192 Å °-0.093 Å °

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