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- PDB-2hb2: Structure of HIV protease 6X mutant in apo form -

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Basic information

Entry
Database: PDB / ID: 2hb2
TitleStructure of HIV protease 6X mutant in apo form
ComponentsProtease
KeywordsHYDROLASE / HIV / protease / retrovirus / aspartyl
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA 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 / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Gag-Pol polyprotein / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHeaslet, H. / Tam, K. / Elder, J.H. / Stout, C.D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Conformational flexibility in the flap domains of ligand-free HIV protease.
Authors: Heaslet, H. / Rosenfeld, R. / Giffin, M. / Lin, Y.C. / Tam, K. / Torbett, B.E. / Elder, J.H. / McRee, D.E. / Stout, C.D.
History
DepositionJun 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 20, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE Mutations at positions 24,46,53,63,77,82 are results of drug resistance selection. The ...SEQUENCE Mutations at positions 24,46,53,63,77,82 are results of drug resistance selection. The Gln7Lys mutation was added to prevent autoproteolysis. The Ser37Asn mutation is strain specific.

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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)10,7501
Polymers10,7501
Non-polymers00
Water37821
1
A: Protease

A: Protease


Theoretical massNumber of molelcules
Total (without water)21,4992
Polymers21,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_776-y+2,-x+2,-z+3/21
Buried area2890 Å2
ΔGint-14 kcal/mol
Surface area10180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)49.671, 49.671, 109.613
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 Protease


Mass: 10749.708 Da / Num. of mol.: 1 / Fragment: residues 500-598 / Mutation: L24I, M46I, F53L, L63P, V77I, V82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: NL4-3 / Gene: gal-pol / Plasmid: PET 21A+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21.DE3, PLYS S
References: UniProt: P03367, UniProt: Q9E3M8*PLUS, HIV-1 retropepsin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 281.16 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 5% PEG 3350, 0.05M Na/K Tartrate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 281.16K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.97944 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2006
RadiationMonochromator: Double crystal, parallel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 2.3→24 Å / Num. all: 6582 / Num. obs: 6506 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.7
Reflection shellHighest resolution: 2.3 Å / Rmerge(I) obs: 0.041 / Mean I/σ(I) obs: 1.2 / Num. unique all: 3241 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
MOSFLMdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→24.218 Å / FOM work R set: 0.775 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.291 329 5 %Random
Rwork0.234 ---
all0.234 6613 --
obs0.291 6506 98.8 %-
Solvent computationBsol: 41.819 Å2
Displacement parametersBiso mean: 46.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.171 Å20 Å20 Å2
2--2.171 Å20 Å2
3----4.343 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms743 0 0 21 764
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3591.5
X-RAY DIFFRACTIONc_scbond_it1.6912
X-RAY DIFFRACTIONc_mcangle_it2.2682
X-RAY DIFFRACTIONc_scangle_it2.4762.5
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.3-2.40.402370.35757794
2.4-2.530.419500.32748798
2.53-2.690.336360.276754790
2.69-2.90.313410.264765806
2.9-3.190.303380.252775813
3.19-3.650.306410.276772813
3.65-4.590.228460.2788834
4.59-24.220.244400.199818858
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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