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- PDB-2pc0: Apo Wild-type HIV Protease in the open conformation -

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Basic information

Entry
Database: PDB / ID: 2pc0
TitleApo Wild-type HIV Protease in the open conformation
ComponentsProtease
KeywordsHYDROLASE / 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 / 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
R-1,2-PROPANEDIOL / Protease / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHeaslet, H. / Rosenfeld, R. / Giffin, M.J. / Elder, J.H. / McRee, D.E. / 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
DepositionMar 29, 2007Deposition 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: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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 1.5Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9323
Polymers10,8321
Non-polymers1002
Water2,018112
1
A: Protease
hetero molecules

A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8646
Polymers21,6642
Non-polymers2014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3360 Å2
ΔGint-34 kcal/mol
Surface area10710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)46.416, 46.416, 101.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Protease


Mass: 10831.833 Da / Num. of mol.: 1 / Mutation: Q7K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: BH10 / Gene: pol / Plasmid: pLys S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21.DE
References: UniProt: A3FH86, 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.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.2 M Magnesium chloride, 20% w/v PEG 3350, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 1, 2006
Details: Double-crystal monochromator, 1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing
RadiationMonochromator: Double crystal, parallel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→20.8 Å / Num. all: 27866 / Num. obs: 22409 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rsym value: 0.057 / Net I/σ(I): 16.5
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 3 / Num. unique all: 1588 / Rsym value: 0.522 / % possible all: 98

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å20.76 Å
Translation2.5 Å20.76 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2AZ8

2az8


Resolution: 1.4→20.8 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.871 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.186 1165 5.2 %RANDOM
Rwork0.153 ---
obs0.155 22398 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.554 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms760 0 6 112 878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022868
X-RAY DIFFRACTIONr_bond_other_d00.02860
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.9951189
X-RAY DIFFRACTIONr_angle_other_deg0.59332007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3255117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.64624.48329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.02515165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.353155
X-RAY DIFFRACTIONr_chiral_restr0.390.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02974
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02157
X-RAY DIFFRACTIONr_nbd_refined0.2960.2116
X-RAY DIFFRACTIONr_nbd_other0.2020.2837
X-RAY DIFFRACTIONr_nbtor_refined0.1660.2432
X-RAY DIFFRACTIONr_nbtor_other0.0860.2518
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.254
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3170.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.223
X-RAY DIFFRACTIONr_mcbond_it2.1511.5720
X-RAY DIFFRACTIONr_mcbond_other1.611.5227
X-RAY DIFFRACTIONr_mcangle_it2.6722907
X-RAY DIFFRACTIONr_scbond_it3.7523361
X-RAY DIFFRACTIONr_scangle_it5.0264.5282
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 82 -
Rwork0.209 1502 -
obs-1584 97.54 %
Refinement TLS params.Method: refined / Origin x: 3.066 Å / Origin y: 4.6361 Å / Origin z: -11.3929 Å
111213212223313233
T-0.0169 Å20.0168 Å2-0.0052 Å2-0.0011 Å20.0036 Å2---0.0262 Å2
L0.2187 °20.1052 °2-0.1084 °2-0.2088 °2-0.2261 °2--0.6463 °2
S-0.0351 Å °-0.0004 Å °-0.0038 Å °-0.0032 Å °0.0249 Å °-0.0077 Å °0.0672 Å °0.096 Å °0.0102 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDAuth seq-IDLabel seq-ID
11001 - 10211 - 21
21022 - 104022 - 40
31041 - 105541 - 55
41056 - 107956 - 79
51080 - 109980 - 99

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