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- PDB-4wx4: Crystal structure of adenovirus 8 protease in complex with a nitr... -

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Basic information

Entry
Database: PDB / ID: 4wx4
TitleCrystal structure of adenovirus 8 protease in complex with a nitrile inhibitor
Components
  • Protease
  • peptide
KeywordsHYDROLASE / cysteine protease / inhibitor / cofactor
Function / homology
Function and homology information


adenain / virion component / cysteine-type endopeptidase activity / host cell nucleus / proteolysis / DNA binding
Similarity search - Function
Peptidase C5, adenain / Adenovirus endoprotease / Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Papain-like cysteine peptidase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3VF / GLYCINE / Protease
Similarity search - Component
Biological speciesHuman adenovirus D serotype 8
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.03 Å
AuthorsGrosche, P. / Sirockin, F. / Mac Sweeney, A. / Ramage, P. / Erbel, P. / Melkko, S. / Bernardi, A. / Hughes, N. / Ellis, D. / Combrink, K. ...Grosche, P. / Sirockin, F. / Mac Sweeney, A. / Ramage, P. / Erbel, P. / Melkko, S. / Bernardi, A. / Hughes, N. / Ellis, D. / Combrink, K. / Jarousse, N. / Altmann, E.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Structure-based design and optimization of potent inhibitors of the adenoviral protease.
Authors: Grosche, P. / Sirockin, F. / Mac Sweeney, A. / Ramage, P. / Erbel, P. / Melkko, S. / Bernardi, A. / Hughes, N. / Ellis, D. / Combrink, K.D. / Jarousse, N. / Altmann, E.
History
DepositionNov 13, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
C: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2355
Polymers24,4382
Non-polymers7973
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint2 kcal/mol
Surface area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.454, 42.790, 59.059
Angle α, β, γ (deg.)90.000, 93.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AC

#1: Protein Protease /


Mass: 23124.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus D serotype 8 / References: UniProt: B9A5C1
#2: Protein/peptide peptide /


Mass: 1313.639 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 253 molecules

#3: Chemical ChemComp-3VF / N-[(2-cyanopyrimidin-4-yl)methyl]-3-[2-(3,5-dichlorophenyl)-2-methylpropanoyl]-4-methoxybenzamide


Mass: 483.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H20Cl2N4O3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Crystallization Reservoir Solution = 0.2M proline, 0.1M HEPES pH 7.5, 10% PEG3350 Crystallization Protein Solution = 5 mg/ml adenain in 20 mM Tris, 100 mM NaCl, pH 7.6. 5 mM inhibitor added.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.03→58.9 Å / Num. obs: 102036 / % possible obs: 85.7 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 11.29 Å2 / Rmerge F obs: 0.029 / Rmerge(I) obs: 0.025 / Rrim(I) all: 0.029 / Χ2: 1.015 / Net I/σ(I): 26.93 / Num. measured all: 273190
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.03-1.061.60.1370.0836.274815753529960.1139.8
1.06-1.090.1030.078.57427728939510.08954.2
1.09-1.120.0880.06511.311827712850130.08270.3
1.12-1.150.0680.0615.0119103694360960.07287.8
1.15-1.190.0580.05617.1820470671860860.06790.6
1.19-1.230.0550.05218.2318929645958920.06291.2
1.23-1.280.0480.04920.3719155625957790.05892.3
1.28-1.330.0420.04322.7119134603356300.05193.3
1.33-1.390.0390.0424.417904579854500.04894
1.39-1.460.0350.03726.3416846552552350.04594.8
1.46-1.540.0280.03330.9217368528350580.03995.7
1.54-1.630.0250.0334.1516253498048120.03596.6
1.63-1.740.0230.02735.8314317470945290.03396.2
1.74-1.880.0210.02539.8714340435342260.0397.1
1.88-2.060.0180.02343.7213480404539460.02897.6
2.06-2.30.0170.02345.3211747365535680.02797.6
2.3-2.660.0170.02245.719974322931470.02697.5
2.66-3.260.0150.02149.189287274726980.02598.2
3.26-4.610.0150.0248.726746214021130.02598.7
4.610.0150.02150.524068121011860.02698

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 1.03→34.79 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.3082 / WRfactor Rwork: 0.2413 / FOM work R set: 0.705 / SU B: 0.482 / SU ML: 0.012 / SU Rfree: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.023 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1365 4371 5 %RANDOM
Rwork0.1172 83041 --
obs0.1182 83041 85.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.37 Å2 / Biso mean: 12.065 Å2 / Biso min: 4.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.1 Å2
2--0 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.03→34.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1587 0 48 250 1885
Biso mean--8.8 22.68 -
Num. residues----212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0191857
X-RAY DIFFRACTIONr_angle_refined_deg2.1941.982524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2985230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.20620.90988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03915307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1241524
X-RAY DIFFRACTIONr_chiral_restr0.160.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211459
X-RAY DIFFRACTIONr_rigid_bond_restr10.66631857
X-RAY DIFFRACTIONr_sphericity_free29.022544
X-RAY DIFFRACTIONr_sphericity_bonded13.76152002
LS refinement shellResolution: 1.03→1.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.157 148 -
Rwork0.128 2809 -
all-2957 -
obs--39.44 %

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