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- PDB-1jq6: HUMAN CYTOMEGALOVIRUS PROTEASE DIMER-INTERFACE MUTANT, S225Y -

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Basic information

Entry
Database: PDB / ID: 1jq6
TitleHUMAN CYTOMEGALOVIRUS PROTEASE DIMER-INTERFACE MUTANT, S225Y
ComponentsASSEMBLIN
KeywordsHYDROLASE / Herpesvirus / cytomegalovirus / serine protease / dimerization / enzyme activity regulation
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
AuthorsBatra, R. / Khayat, R. / Tong, L.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Molecular mechanism for dimerization to regulate the catalytic activity of human cytomegalovirus protease.
Authors: Batra, R. / Khayat, R. / Tong, L.
History
DepositionAug 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASSEMBLIN


Theoretical massNumber of molelcules
Total (without water)28,5191
Polymers28,5191
Non-polymers00
Water75742
1
A: ASSEMBLIN

A: ASSEMBLIN


Theoretical massNumber of molelcules
Total (without water)57,0372
Polymers57,0372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2260 Å2
ΔGint-23 kcal/mol
Surface area16690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)42.270, 108.300, 108.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsMonomer in the asymmetric unit, but biological assembly unit is a dimer that can be generated by the two fold axis.

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Components

#1: Protein ASSEMBLIN / PROTEASE


Mass: 28518.590 Da / Num. of mol.: 1 / Mutation: A143Q, S225Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 5 / Genus: Cytomegalovirus / Production host: Escherichia coli (E. coli) / References: UniProt: P16753, assemblin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: PEG 8000, sodium cacodylate, magnesium acetate, glycerol, spermine tetrahydrochloride, DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 %(w/v)PEG80001reservoir
20.1 Msodium cacodylate1reservoir
30.15 M1reservoirMgAc2
42.5 %(v/v)glycerol1reservoir
520 mMspermine tetrahydrochloride1reservoir
62 mMdithiothreitol1reservoir
725 mg/mlprotein1drop
820 mM1dropNaAc
90.1 mMEDTA1drop
101 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.976 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Nov 9, 2000
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3→19.3 Å / Num. all: 38153 / Num. obs: 10420 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 18.5 Å2
Reflection shellResolution: 2.3→2.44 Å / % possible all: 93
Reflection
*PLUS
% possible obs: 91 % / Num. measured all: 38153 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Rmerge(I) obs: 0.172

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Processing

Software
NameVersionClassification
COMOphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WPO (monomer)

1wpo


Resolution: 2.3→19.3 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 5293688.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 793 7.6 %RANDOM
Rwork0.229 ---
all0.236 38153 --
obs-10420 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.4329 Å2 / ksol: 0.394661 e/Å3
Displacement parametersBiso mean: 43.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2--14.63 Å20 Å2
3----13.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1336 0 0 42 1378
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_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.591.5
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it3.162.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 118 7.5 %
Rwork0.249 1465 -
obs-1070 84.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM.DAT
X-RAY DIFFRACTION3WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 7.6 % / Rfactor obs: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 43.2 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_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
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: 0.284 / % reflection Rfree: 7.5 % / Rfactor Rwork: 0.249

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