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- PDB-2hb4: Structure of HIV Protease NL4-3 in an Unliganded State -

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Basic information

Entry
Database: PDB / ID: 2hb4
TitleStructure of HIV Protease NL4-3 in an Unliganded State
ComponentsProtease
KeywordsHYDROLASE / HIV / protease / aspartyl / retrovirus
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 / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / 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 / symbiont-mediated suppression of host gene expression / 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. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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
R-1,2-PROPANEDIOL / Gag-Pol polyprotein / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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: Advisory / Derived calculations / Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0845
Polymers10,8321
Non-polymers2534
Water73941
1
A: Protease
hetero molecules

A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,16910
Polymers21,6642
Non-polymers5058
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area4030 Å2
ΔGint-6 kcal/mol
Surface area10180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)48.985, 48.985, 105.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-101-

MG

21A-928-

HOH

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Components

#1: Protein Protease /


Mass: 10831.833 Da / Num. of mol.: 1 / Fragment: residues 500-598 / Mutation: Q7K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: NL4-3 / Gene: gag-pol / Plasmid: PET 21A+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21.DE3, PLYS S
References: UniProt: P03367, UniProt: Q903N5*PLUS, HIV-1 retropepsin
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 281.16 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris HCl, 0.2M MgCl2, 15% PEG 8K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281.16K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: May 2, 2006 / Details: Rigaku VariMax HF Confocal Mirror
RadiationMonochromator: Rigaku VariMax HF Confocal Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→44.44 Å / Num. all: 13572 / Num. obs: 13526 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 7.34 % / Rmerge(I) obs: 0.095 / Χ2: 1.01 / Net I/σ(I): 8.9 / Scaling rejects: 751
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 7.24 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 2.2 / Num. measured all: 9663 / Num. unique all: 1334 / Χ2: 1.14 / % possible all: 99.5

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Phasing

Phasing MRRfactor: 0.599 / Cor.coef. Fo:Fc: 0.258
Highest resolutionLowest resolution
Rotation3 Å35.91 Å
Translation3 Å35.91 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
MOLREPphasing
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata reduction
d*TREK9.4SSIdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→44.46 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 10.862 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32073 393 5.3 %RANDOM
Rwork0.23409 ---
obs0.23834 7074 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.072 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20 Å2
2--0.8 Å20 Å2
3----1.6 Å2
Refinement stepCycle: LAST / Resolution: 2.15→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms760 0 16 41 817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022808
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0342.0021096
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.265104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.98825.17229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.11715146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.376154
X-RAY DIFFRACTIONr_chiral_restr0.1680.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02588
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.2291
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2538
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.241
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3270.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.541.5527
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.5392824
X-RAY DIFFRACTIONr_scbond_it5.6773323
X-RAY DIFFRACTIONr_scangle_it7.6134.5272
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.529 26 -
Rwork0.378 500 -
obs--98.87 %
Refinement TLS params.Method: refined / Origin x: 5.3267 Å / Origin y: -5.2528 Å / Origin z: 15.0909 Å
111213212223313233
T0.0118 Å2-0.0227 Å20.0373 Å2--0.0295 Å2-0.0053 Å2---0.0267 Å2
L0.5841 °2-0.0234 °2-0.5132 °2-0.4703 °2-0.0797 °2--0.8671 °2
S-0.0603 Å °0.0265 Å °-0.0229 Å °-0.1635 Å °0.085 Å °-0.0834 Å °0.0238 Å °-0.1604 Å °-0.0246 Å °
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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