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- PDB-6a4v: Open Reading frame 49 -

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Basic information

Entry
Database: PDB / ID: 6a4v
TitleOpen Reading frame 49
Components49 protein
KeywordsREPLICATION / Gamma herpesvirus 68 Open reading frame 49 / ORF49 Poly (ADP-ribose) polymerase-1 (PARP-1)
Function / homologyBRRF1, herpesviridae / BRRF1-like protein / 49 protein
Function and homology information
Biological speciesMurid herpesvirus 4 (Murine herpesvirus 68)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsHwang, K.Y. / Song, M.J. / Kim, J.S. / Cheong, W.C.
CitationJournal: Iucrj / Year: 2018
Title: Structure-based mechanism of action of a viral poly(ADP-ribose) polymerase 1-interacting protein facilitating virus replication.
Authors: Chung, W.C. / Kim, J. / Kim, B.C. / Kang, H.R. / Son, J. / Ki, H. / Hwang, K.Y. / Song, M.J.
History
DepositionJun 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
SupersessionDec 18, 2019ID: 5YX5
Revision 1.1Dec 18, 2019Group: Advisory / Database references
Category: citation / citation_author / pdbx_database_PDB_obs_spr
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 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: 49 protein
B: 49 protein


Theoretical massNumber of molelcules
Total (without water)76,4042
Polymers76,4042
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-18 kcal/mol
Surface area25560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.179, 134.179, 157.158
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein 49 protein / ORF49 protein


Mass: 38201.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid herpesvirus 4 (Murine herpesvirus 68)
Gene: BNLF1, 49, GAMMAHV.ORF49 / Production host: Escherichia coli (E. coli) / References: UniProt: P88987
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 5.34 Å3/Da / Density % sol: 76.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.1M Tris-Hcl (pH 8.2), 0.33M sodium/potassium tartrate 0.5% polyehylene glycerol 5000 mono-methyl ether

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.9
11-K, -H, -L20.1
ReflectionResolution: 2.2→30 Å / Num. obs: 272254 / % possible obs: 90.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 51.49 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 11.94
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.414 / Num. unique obs: 7618

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→29.82 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.91 / SU B: 2.682 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.031 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27436 4069 5 %RANDOM
Rwork0.2393 ---
obs0.241 77108 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.832 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2--1.3 Å20 Å2
3----2.61 Å2
Refinement stepCycle: 1 / Resolution: 2.2→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 0 60 4440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0144466
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174110
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.6356054
X-RAY DIFFRACTIONr_angle_other_deg1.1071.6279596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3315533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80123.125224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.30815811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4811520
X-RAY DIFFRACTIONr_chiral_restr0.0960.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024857
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02839
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_it6.5945.3752150
X-RAY DIFFRACTIONr_mcbond_other6.5915.3732149
X-RAY DIFFRACTIONr_mcangle_it8.8068.0332677
X-RAY DIFFRACTIONr_mcangle_other8.8068.0362678
X-RAY DIFFRACTIONr_scbond_it7.1835.9192316
X-RAY DIFFRACTIONr_scbond_other7.1835.9192316
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.018.6453378
X-RAY DIFFRACTIONr_long_range_B_refined12.6363.6955256
X-RAY DIFFRACTIONr_long_range_B_other12.63463.7045254
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.201→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 281 -
Rwork0.323 5276 -
obs--91.4 %

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