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- PDB-1t6l: Crystal Structure of the Human Cytomegalovirus DNA Polymerase Sub... -

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Basic information

Entry
Database: PDB / ID: 1t6l
TitleCrystal Structure of the Human Cytomegalovirus DNA Polymerase Subunit, UL44
ComponentsDNA polymerase processivity factor
KeywordsREPLICATION / Processivity Fold
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / DNA polymerase processivity factor activity / virion component / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / DNA replication / virus-mediated perturbation of host defense response / host cell nucleus / DNA binding
Similarity search - Function
Herpesvirus polymerase accessory protein / Herpesvirus polymerase accessory protein / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / : / Alpha Beta
Similarity search - Domain/homology
DNA polymerase processivity factor
Similarity search - Component
Biological speciesHuman herpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsAppleton, B.A. / Loregian, A. / Filman, D.J. / Coen, D.M. / Hogle, J.M.
CitationJournal: Mol.Cell / Year: 2004
Title: The Cytomegalovirus DNA Polymerase Subunit UL44 Forms a C Clamp-Shaped Dimer.
Authors: Appleton, B.A. / Loregian, A. / Filman, D.J. / Coen, D.M. / Hogle, J.M.
History
DepositionMay 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE author state that the SER 205 is indeed correct and it may represent a different isolate ...SEQUENCE author state that the SER 205 is indeed correct and it may represent a different isolate cytomegalovirus, referring to Ertl PF, Powell KL. "Physical and functional interaction of human cytomegalovirus DNA polymerase and its accessory protein (ICP36) expressed in insect cells." J Virol. 1992 Jul;66(7):4126-33.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase processivity factor


Theoretical massNumber of molelcules
Total (without water)32,5771
Polymers32,5771
Non-polymers00
Water1,71195
1
A: DNA polymerase processivity factor

A: DNA polymerase processivity factor


Theoretical massNumber of molelcules
Total (without water)65,1532
Polymers65,1532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Unit cell
Length a, b, c (Å)53.930, 53.930, 340.067
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe biological assembly is a dimer is a dimer generated by the two fold axis: x, x-y, 1/6-z

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Components

#1: Protein DNA polymerase processivity factor / Polymerase accessory protein / PAP / ICP36 protein


Mass: 32576.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 5 / Genus: Cytomegalovirus / Gene: UL44 / Plasmid details: (Glutathione S-transferase; Invitrogen) / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P16790
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: polyethylene glycol 4000, sodium acetate, sodium chloride, dithiothreitol , pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12C10.9786, 0.9788, 0.9500
SYNCHROTRONNSLS X12C20.9786, 0.9787, 0.9500, 1.010
SYNCHROTRONAPS 14-BM-C30.9
Detector
TypeIDDetectorDate
BRANDEIS - B41CCDJul 23, 2002
BRANDEIS - B42CCDJul 24, 2002
ADSC QUANTUM 43CCDMar 9, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111)MADMx-ray1
2Si (111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.97881
30.951
40.97871
51.011
60.91
ReflectionResolution: 1.85→30 Å / Num. all: 26651 / Num. obs: 26592 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 28.8 % / Biso Wilson estimate: 25.8 Å2 / Rsym value: 0.056 / Net I/σ(I): 58.4
Reflection shellResolution: 1.85→1.93 Å / Redundancy: 18 % / Mean I/σ(I) obs: 14.2 / Num. unique all: 3215 / Rsym value: 0.267 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→12 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.081 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.163 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2683 10.2 %RANDOM
Rwork0.23487 ---
all0.23831 23673 --
obs0.23831 23673 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.465 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.12 Å20 Å2
2--0.23 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.85→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 0 95 2036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221980
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.9552692
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4845247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1180.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021445
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.2798
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6520.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1251.51247
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0522040
X-RAY DIFFRACTIONr_scbond_it2.6453733
X-RAY DIFFRACTIONr_scangle_it4.1714.5652
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.948 Å / Total num. of bins used: 10
RfactorNum. reflection
Rfree0.297 394
Rwork0.238 3279
obs-3279

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