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- PDB-1dml: CRYSTAL STRUCTURE OF HERPES SIMPLEX UL42 BOUND TO THE C-TERMINUS ... -

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Basic information

Entry
Database: PDB / ID: 1dml
TitleCRYSTAL STRUCTURE OF HERPES SIMPLEX UL42 BOUND TO THE C-TERMINUS OF HSV POL
Components
  • DNA POLYMERASE
  • DNA POLYMERASE PROCESSIVITY FACTOR
KeywordsDNA BINDING PROTEIN/TRANSFERASE / herpes simplex virus / dna synthesis / sliding clamps / PCNA / processivity / DNA BINDING PROTEIN-TRANSFERASE COMPLEX
Function / homology
Function and homology information


DNA polymerase complex / bidirectional double-stranded viral DNA replication / viral DNA genome replication / ribonuclease H / DNA polymerase processivity factor activity / DNA-templated DNA replication / RNA-DNA hybrid ribonuclease activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication ...DNA polymerase complex / bidirectional double-stranded viral DNA replication / viral DNA genome replication / ribonuclease H / DNA polymerase processivity factor activity / DNA-templated DNA replication / RNA-DNA hybrid ribonuclease activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / nucleotide binding / host cell nucleus / DNA binding
Similarity search - Function
DNA polymerase processivity factor (UL42) / DNA polymerase processivity factor (UL42) / DNA polymerase catalytic subunit Pol, C-terminal / DNA polymerase catalytic subunit Pol / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / : / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain ...DNA polymerase processivity factor (UL42) / DNA polymerase processivity factor (UL42) / DNA polymerase catalytic subunit Pol, C-terminal / DNA polymerase catalytic subunit Pol / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / : / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / : / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha Beta
Similarity search - Domain/homology
DNA polymerase catalytic subunit / DNA polymerase processivity factor
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsZuccola, H.J. / Filman, D.J. / Coen, D.M. / Hogle, J.M.
CitationJournal: Mol.Cell / Year: 2000
Title: The crystal structure of an unusual processivity factor, herpes simplex virus UL42, bound to the C terminus of its cognate polymerase.
Authors: Zuccola, H.J. / Filman, D.J. / Coen, D.M. / Hogle, J.M.
History
DepositionDec 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA POLYMERASE PROCESSIVITY FACTOR
B: DNA POLYMERASE
C: DNA POLYMERASE PROCESSIVITY FACTOR
D: DNA POLYMERASE
E: DNA POLYMERASE PROCESSIVITY FACTOR
F: DNA POLYMERASE
G: DNA POLYMERASE PROCESSIVITY FACTOR
H: DNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)151,9328
Polymers151,9328
Non-polymers00
Water00
1
A: DNA POLYMERASE PROCESSIVITY FACTOR
B: DNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)37,9832
Polymers37,9832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-18 kcal/mol
Surface area13910 Å2
MethodPISA
2
C: DNA POLYMERASE PROCESSIVITY FACTOR
D: DNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)37,9832
Polymers37,9832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-18 kcal/mol
Surface area14330 Å2
MethodPISA
3
E: DNA POLYMERASE PROCESSIVITY FACTOR
F: DNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)37,9832
Polymers37,9832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-17 kcal/mol
Surface area14340 Å2
MethodPISA
4
G: DNA POLYMERASE PROCESSIVITY FACTOR
H: DNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)37,9832
Polymers37,9832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-18 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.320, 100.070, 129.530
Angle α, β, γ (deg.)90.00, 100.62, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a heterodimer of UL42 and HSV Polymerase

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Components

#1: Protein
DNA POLYMERASE PROCESSIVITY FACTOR / DNA-BINDING PROTEIN UL42


Mass: 34231.879 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Genus: Simplexvirus / Plasmid: PMAL-C / Production host: Escherichia coli (E. coli) / References: UniProt: P10226
#2: Protein/peptide
DNA POLYMERASE


Mass: 3751.197 Da / Num. of mol.: 4 / Fragment: C-TERMINAL 36 AMINO ACIDS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Genus: Simplexvirus / Plasmid: PGEX6P1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07917, DNA-directed DNA polymerase

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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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5
Details: PEGMME 5000, pH 7.5, vapor diffusion, temperature 22K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-10 mg/mlprotein1drop
210-14 %mPEG50001reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 22, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→29.87 Å / Num. all: 37576 / Num. obs: 37917 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.244 / Num. unique all: 37217 / % possible all: 99.8
Reflection
*PLUS
Num. obs: 37576 / Num. measured all: 260475
Reflection shell
*PLUS
% possible obs: 99.8 % / Mean I/σ(I) obs: 6.1

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.7→12 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3153280.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 3657 10.1 %RANDOM
Rwork0.23 ---
all0.23 37534 --
obs0.23 36258 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.41 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.47 Å20 Å2-3.24 Å2
2---1.87 Å20 Å2
3---7.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-6 Å
Luzzati sigma a0.46 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.7→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9414 0 0 0 9414
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it2.841.5
X-RAY DIFFRACTIONc_mcangle_it4.62
X-RAY DIFFRACTIONc_scbond_it4.182
X-RAY DIFFRACTIONc_scangle_it5.872.5
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 611 10.5 %
Rwork0.291 5217 -
obs--93.6 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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