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- PDB-4piq: Crystal structure of human adenovirus 8 protease with a nitrile i... -

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Basic information

Entry
Database: PDB / ID: 4piq
TitleCrystal structure of human adenovirus 8 protease with a nitrile inhibitor
Components
  • PVI
  • Protease
KeywordsHydrolase/Hydrolase inhibitor / Adenain / adenovirus / cysteine protease / pVIc / cofactor / inhibitor / Hydrolase-Hydrolase inhibitor complex
Function / homology
Function and homology information


adenain / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / virion component / viral capsid / host cell cytoplasm / cysteine-type endopeptidase activity / host cell nucleus ...adenain / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / virion component / viral capsid / host cell cytoplasm / cysteine-type endopeptidase activity / host cell nucleus / proteolysis / DNA binding
Similarity search - Function
Peptidase C5, adenain / Adenovirus endoprotease / Minor capsid protein VI / Minor capsid protein VI / Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Papain-like cysteine peptidase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3FS / Pre-protein VI / Protease
Similarity search - Component
Biological speciesHuman adenovirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsMac Sweeney, A. / Grosche, P. / Ellis, D. / Combrink, K. / Erbel, P. / Hughes, N. / Sirockin, F. / Melkko, S. / Bernardi, A. / Ramage, P. ...Mac Sweeney, A. / Grosche, P. / Ellis, D. / Combrink, K. / Erbel, P. / Hughes, N. / Sirockin, F. / Melkko, S. / Bernardi, A. / Ramage, P. / Jarousse, N. / Altmann, E.
CitationJournal: Acs Med.Chem.Lett. / Year: 2014
Title: Discovery and structure-based optimization of adenain inhibitors.
Authors: Mac Sweeney, A. / Grosche, P. / Ellis, D. / Combrink, K. / Erbel, P. / Hughes, N. / Sirockin, F. / Melkko, S. / Bernardi, A. / Ramage, P. / Jarousse, N. / Altmann, E.
History
DepositionMay 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen ...diffrn_detector / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease
B: PVI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7673
Polymers24,3642
Non-polymers4031
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-4 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.269, 42.269, 193.784
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Protease /


Mass: 22993.312 Da / Num. of mol.: 1 / Fragment: UNP residues 2-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 8 / Gene: L3 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: B9A5C1
#2: Protein/peptide PVI


Mass: 1370.691 Da / Num. of mol.: 1 / Fragment: UNP residues 223-233 / Source method: obtained synthetically / Source: (synth.) Human adenovirus 8 / References: UniProt: B9A5B9
#3: Chemical ChemComp-3FS / N-[(3,5-dichlorophenyl)acetyl]-L-threonyl-N-[(2Z)-2-iminoethyl]glycinamide


Type: peptide-like / Mass: 403.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20Cl2N4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.05 Å3/Da / Density % sol: 40.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium potassium tartrate, 20% PEG3350. Crystals soaked 5 hours in buffer containing 2 mM inhibitor

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→34.24 Å / Num. obs: 11953 / % possible obs: 91.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 42.17 Å2 / Rmerge F obs: 0.081 / Rmerge(I) obs: 0.032 / Rrim(I) all: 0.041 / Χ2: 1.087 / Net I/σ(I): 14.08 / Num. measured all: 22958
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.07-2.120.4540.2042.9817849449140.26496.8
2.12-2.180.4060.1833.4716378938340.23493.4
2.18-2.250.6120.1942.6716369078570.24994.5
2.25-2.310.2510.1235.3514398577240.15884.5
2.31-2.390.2040.1016.1514758487830.1392.3
2.39-2.470.1720.097.3515778367950.11495.1
2.47-2.570.1170.0659.914417617320.08296.2
2.57-2.670.0990.05811.0414467867390.07494
2.67-2.790.0820.05113.3513417366890.06493.6
2.79-2.930.0620.04315.3712156976360.05591.2
2.93-3.090.0490.03719.0310836825940.04787.1
3.09-3.270.0360.03222.3611496385960.0493.4
3.27-3.50.0310.02924.610876085670.03793.3
3.5-3.780.0260.02525.959895655210.03292.2
3.78-4.140.0240.02428.148825324670.0387.8
4.14-4.630.0220.02428.786914874060.0383.4
4.63-5.340.020.02331.387564343900.0389.9
5.34-6.550.0160.01830.746123653140.02486
6.55-9.260.0150.01431.484493072510.01981.8
9.260.0120.01133.382691891440.01576.2

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Processing

Software
NameVersionClassification
XDSdata reduction
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
BUSTER2.11.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→34.24 Å / Cor.coef. Fo:Fc: 0.9369 / Cor.coef. Fo:Fc free: 0.8752 / SU R Cruickshank DPI: 0.326 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.367 / SU Rfree Blow DPI: 0.274 / SU Rfree Cruickshank DPI: 0.266
RfactorNum. reflection% reflectionSelection details
Rfree0.3188 597 5 %RANDOM
Rwork0.2422 ---
obs0.246 11947 91.44 %-
Displacement parametersBiso max: 115.2 Å2 / Biso mean: 40.24 Å2 / Biso min: 18.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.7782 Å20 Å20 Å2
2--0.7782 Å20 Å2
3----1.5564 Å2
Refine analyzeLuzzati coordinate error obs: 0.416 Å
Refinement stepCycle: final / Resolution: 2.07→34.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 26 92 1815
Biso mean--50 40.92 -
Num. residues----215
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d629SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes35HARMONIC2
X-RAY DIFFRACTIONt_gen_planes276HARMONIC5
X-RAY DIFFRACTIONt_it1801HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion218SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2036SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1801HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2435HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion18.6
LS refinement shellResolution: 2.07→2.27 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4091 142 5 %
Rwork0.3306 2697 -
all0.3346 2839 -
obs--91.44 %

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