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- PDB-4z4x: Crystal Structure of Multidrug Resistant HIV-1 Protease Clinical ... -

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Basic information

Entry
Database: PDB / ID: 4z4x
TitleCrystal Structure of Multidrug Resistant HIV-1 Protease Clinical Isolate PR20D25N with Open Flap
ComponentsProtease
KeywordsHYDROLASE / HIV-1 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 / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Retropepsin-like catalytic domain / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsChang, Y.C. / Shen, C.-H. / Weber, I.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01GM062920 United States
CitationJournal: J.Mol.Graph.Model. / Year: 2015
Title: Conformational variation of an extreme drug resistant mutant of HIV protease.
Authors: Shen, C.H. / Chang, Y.C. / Agniswamy, J. / Harrison, R.W. / Weber, I.T.
History
DepositionApr 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease


Theoretical massNumber of molelcules
Total (without water)21,5312
Polymers21,5312
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-17 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.522, 45.522, 104.148
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Protease


Mass: 10765.558 Da / Num. of mol.: 2
Mutation: Q7K, L10F, I13V, I15V, D25N, D30N, V32I, L33F, E35D, M36I, S37N, I47V, I54L, Q58E, I62V, L63P, A71V, I84V, N88D, L89T and L90M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0PQ60
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9 / Details: 0.2M magnesium chloride and 20% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 28, 2011
RadiationMonochromator: SI 220 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.75→41.71 Å / Num. obs: 21444 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.9
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 4.5 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
MOLREP10.2.35phasing
HKL-2000data scaling
SERGUIdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AOI

2aoi


Resolution: 1.75→41.71 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.527 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21687 1069 5.1 %RANDOM
Rwork0.18434 ---
obs0.18599 19784 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.826 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å2-0 Å2
2---0.09 Å2-0 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.75→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 0 110 1628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0191555
X-RAY DIFFRACTIONr_bond_other_d0.0020.021573
X-RAY DIFFRACTIONr_angle_refined_deg2.5061.9692114
X-RAY DIFFRACTIONr_angle_other_deg1.24833614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4745198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.07724.48358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52415266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.919158
X-RAY DIFFRACTIONr_chiral_restr0.1870.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211742
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02334
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4531.364795
X-RAY DIFFRACTIONr_mcbond_other1.4421.363794
X-RAY DIFFRACTIONr_mcangle_it2.1562.043992
X-RAY DIFFRACTIONr_mcangle_other2.1592.044993
X-RAY DIFFRACTIONr_scbond_it2.5141.712760
X-RAY DIFFRACTIONr_scbond_other2.5141.712760
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8772.4291122
X-RAY DIFFRACTIONr_long_range_B_refined5.06611.8181633
X-RAY DIFFRACTIONr_long_range_B_other5.03111.5751589
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.747→1.793 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 77 -
Rwork0.238 1430 -
obs--96.23 %
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)
10.27580.0772-0.48520.5890.01181.5007-0.0006-0.04270.00940.0997-0.0361-0.00170.12280.07160.03670.03940.00520.00550.0195-0.00410.00618.579-2.73911.286
20.65790.1847-0.00510.2390.44941.4291-0.04730.0849-0.0121-0.0451-0.0031-0.0051-0.0719-0.10730.05040.01990.00980.00350.0364-0.0070.009320.059-4.288-11.789
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 99
2X-RAY DIFFRACTION2B101 - 199

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