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- PDB-1ief: CRYSTAL STRUCTURE OF THE CATALYTIC SITE MUTANT S134A OF THE HUMAN... -

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Basic information

Entry
Database: PDB / ID: 1ief
TitleCRYSTAL STRUCTURE OF THE CATALYTIC SITE MUTANT S134A OF THE HUMAN CYTOMEGALOVIRUS PROTEASE
ComponentsCAPSID PROTEIN P40: ASSEMBLIN PROTEASE
KeywordsHYDROLASE / COAT PROTEIN / SERINE PROTEASE / CATALYTIC TRIAD / VIRAL PROTEASE
Function / homology
Function and homology information


assemblin / nuclear capsid assembly / viral release from host cell / host cell cytoplasm / serine-type endopeptidase activity / host cell nucleus / proteolysis / identical protein binding
Similarity search - Function
Serine Protease, Human Cytomegalovirus Protease; Chain A / Herpesvirus/Caudovirus protease domain / Peptidase S21 / Herpesvirus protease superfamily / Assemblin (Peptidase family S21) / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKhayat, R. / Batra, R. / Massariol, M.J. / Lagace, L. / Tong, L.
CitationJournal: Biochemistry / Year: 2001
Title: Investigating the role of histidine 157 in the catalytic activity of human cytomegalovirus protease.
Authors: Khayat, R. / Batra, R. / Massariol, M.J. / Lagace, L. / Tong, L.
History
DepositionApr 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAPSID PROTEIN P40: ASSEMBLIN PROTEASE
B: CAPSID PROTEIN P40: ASSEMBLIN PROTEASE


Theoretical massNumber of molelcules
Total (without water)56,2292
Polymers56,2292
Non-polymers00
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-16 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.400, 76.400, 171.800
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 CAPSID PROTEIN P40: ASSEMBLIN PROTEASE / HCMV PROTEASE


Mass: 28114.547 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-256 / Mutation: A143Q, S134A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 5 / Genus: Cytomegalovirus / Strain: AD169 / Gene: UL80 / Production host: Escherichia coli (E. coli) / References: UniProt: P16753, assemblin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG3350, 0.1M MES 6.0, 15% GLYCEROL, 5% t-BuOH, 0.3M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlprotein1drop
220 mM1dropNaOAc
380 mM1dropNaCl
419-21 %PEG33501reservoir
50.1 MMES1reservoir
615 %glycerol1reservoir
75 %tert-butyl alcohol1reservoir
80.3-0.4 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 20, 2000
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 23357 / Num. obs: 23000 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.05 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.73
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.92 % / Rmerge(I) obs: 0.154 / % possible all: 96.4
Reflection
*PLUS
Num. measured all: 108421 / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
GLRFphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.34 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4040832.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: THE SIDECHAIN OF HIS157 IS DISORDERED IN BOTH MONOMERS. THEREFORE, ONLY THE ORDERED PORTION IS SHOWN.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1662 7.3 %RANDOM
Rwork0.229 ---
all0.229 22930 --
obs0.229 22695 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.76 Å2 / ksol: 0.398 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.29 Å20 Å20 Å2
2---7.29 Å20 Å2
3---14.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3343 0 0 241 3584
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.582
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 256 7.3 %
Rwork0.238 3228 -
obs-3228 91.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 1 / % reflection Rfree: 7.3 % / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.291 / % reflection Rfree: 7.3 % / Rfactor Rwork: 0.238

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