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- PDB-7dpq: HIV-1 Protease D30N mutant -

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Basic information

Entry
Database: PDB / ID: 7dpq
TitleHIV-1 Protease D30N mutant
ComponentsProtease
KeywordsVIRAL PROTEIN / HIV Protease
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Retropepsin-like catalytic domain / 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
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBihani, S.C. / Hosur, M.V.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2021
Title: Molecular basis for reduced cleavage activity and drug resistance in D30N HIV-1 protease.
Authors: Bihani, S.C. / Gupta, G.D. / Hosur, M.V.
History
DepositionDec 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)21,9331
Polymers21,9331
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9850 Å2
Unit cell
Length a, b, c (Å)62.370, 62.370, 82.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Protease / / Retropepsin


Mass: 21932.789 Da / Num. of mol.: 1 / Mutation: D30N, C95M, D1030N, A1095M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: Q72874
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 1-5% Saturated Ammonium Sulfate, 200 mM /100 mM Phosphate Citrate Buffer pH 6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.65→45.16 Å / Num. obs: 21751 / % possible obs: 99.5 % / Redundancy: 5.6 % / Biso Wilson estimate: 19.57 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 24.23
Reflection shellResolution: 1.65→1.75 Å / Rmerge(I) obs: 0.581 / Num. unique obs: 3438

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kt2

3kt2


Resolution: 1.65→45.16 Å / SU ML: 0.2041 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.2743
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2254 1088 5 %
Rwork0.1914 20660 -
obs0.1931 21748 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.75 Å2
Refinement stepCycle: LAST / Resolution: 1.65→45.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 0 178 1694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061542
X-RAY DIFFRACTIONf_angle_d0.87842089
X-RAY DIFFRACTIONf_chiral_restr0.0606250
X-RAY DIFFRACTIONf_plane_restr0.0054261
X-RAY DIFFRACTIONf_dihedral_angle_d16.9089582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.730.28831340.23942545X-RAY DIFFRACTION98.57
1.73-1.820.30861350.2272566X-RAY DIFFRACTION99.96
1.82-1.930.24581360.20732594X-RAY DIFFRACTION99.96
1.93-2.080.25991370.19082592X-RAY DIFFRACTION100
2.08-2.290.20611360.19142587X-RAY DIFFRACTION100
2.29-2.620.23941360.19582587X-RAY DIFFRACTION100
2.62-3.30.22781370.19362605X-RAY DIFFRACTION100
3.3-45.160.19591370.17522584X-RAY DIFFRACTION98.44
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.739956604430.5242416943211.373438559151.019302014710.4150074035782.243136811250.03276664603440.314650222832-0.199613587273-0.07797793167780.04862903178560.01667512161890.1061625157790.158742361561-0.02291657938560.118894614671-0.0099073833913-0.00325263795640.149009938583-0.02401343443660.127580339088-17.231283649916.792637888519.1194785292
21.894377838121.254677284740.7815566056072.093242689561.212424092981.895947754890.117033654009-0.091713522253-0.09339050520680.280200844236-0.0333619251624-0.224905994150.2074269721260.0370374849246-0.0401413959890.139604053507-0.00935244290569-0.022393718960.1293353796010.0113695036340.136645045763-5.9671553879923.32115677536.4767409675
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 99 )1 - 991 - 99
22chain 'A' and (resid 1001 through 1099 )1001 - 1099100 - 198

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