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- PDB-3i2m: The Crystal Structure of PF-8, the DNA Polymerase Accessory Subun... -

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Basic information

Entry
Database: PDB / ID: 3i2m
TitleThe Crystal Structure of PF-8, the DNA Polymerase Accessory Subunit from Kaposi s Sarcoma-Associated Herpesvirus
ComponentsORF59
KeywordsREPLICATION / processivity
Function / homologyDNA polymerase processivity factor, herpesviridae / Herpes DNA replication accessory factor / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Alpha Beta / Core gene UL42 family protein
Function and homology information
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.81 Å
AuthorsBaltz, J.L. / Filman, D.J. / Ciustea, M. / Silverman, J.E.Y. / Lautenschlager, C.L. / Coen, D.M. / Ricciardi, R.P. / Hogle, J.M.
CitationJournal: J.Virol. / Year: 2009
Title: The crystal structure of PF-8, the DNA polymerase accessory subunit from Kaposi's sarcoma-associated herpesvirus.
Authors: Baltz, J.L. / Filman, D.J. / Ciustea, M. / Silverman, J.E. / Lautenschlager, C.L. / Coen, D.M. / Ricciardi, R.P. / Hogle, J.M.
History
DepositionJun 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: ORF59


Theoretical massNumber of molelcules
Total (without water)33,4151
Polymers33,4151
Non-polymers00
Water00
1
X: ORF59

X: ORF59


Theoretical massNumber of molelcules
Total (without water)66,8292
Polymers66,8292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_546x,x-y-1,-z+7/61
Buried area1570 Å2
ΔGint-7 kcal/mol
Surface area25700 Å2
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.300, 58.300, 386.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein ORF59


Mass: 33414.641 Da / Num. of mol.: 1 / Fragment: UNP residues 2-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q77ZG5

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 18% PEG 3350, 100 mM Tris HCl pH 8.2, 0.2 M lithium chloride, and 20 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 10612 / Num. obs: 10103 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 18.012
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 0.049 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.492 / % possible all: 62.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.5.0093refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.81→29.15 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.917 / SU B: 36.824 / SU ML: 0.324 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.284 / ESU R Free: 0.391
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.28131 465 4.8 %RANDOM
Rwork0.25169 ---
obs0.25311 9267 96.33 %-
all-10103 --
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: 31.36 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å21.33 Å20 Å2
2--2.66 Å20 Å2
3----3.98 Å2
Refinement stepCycle: LAST / Resolution: 2.81→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2145 0 0 0 2145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222183
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8391.9522964
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.65286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.99623.07778
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.09315358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.761513
X-RAY DIFFRACTIONr_chiral_restr0.1250.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0211587
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.76421415
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4842282
X-RAY DIFFRACTIONr_scbond_it1.4424768
X-RAY DIFFRACTIONr_scangle_it2.5226682
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.81→2.956 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.434 49 -
Rwork0.363 823 -
obs-823 86.85 %
Refinement TLS params.Method: refined / Origin x: 27.7329 Å / Origin y: -14.1581 Å / Origin z: 203.4016 Å
111213212223313233
T0.251 Å20.0206 Å20.0437 Å2-0.122 Å2-0.065 Å2--0.2145 Å2
L5.6048 °23.0278 °24.2485 °2-2.512 °22.9444 °2--5.6879 °2
S-0.1454 Å °0.3427 Å °0.2023 Å °-0.2688 Å °-0.077 Å °0.1615 Å °-0.2708 Å °0.1206 Å °0.2225 Å °

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