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- PDB-3rj2: Structural and functional characterization of a novel histone H3 ... -

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Basic information

Entry
Database: PDB / ID: 3rj2
TitleStructural and functional characterization of a novel histone H3 binding protein ORF158L from the Singapore grouper iridovirus (SGIV)
ComponentsPutative uncharacterized protein
KeywordsPROTEIN BINDING / histone 3
Function / homologyJelly Rolls - #1150 / Jelly Rolls / Sandwich / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesSingapore grouper iridovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsChen, L. / Liu, Y. / Sivaraman, J. / Hew, C.L.
CitationJournal: J.Virol. / Year: 2011
Title: Novel histone H3 binding protein ORF158L from the Singapore grouper iridovirus
Authors: Tran, B.N. / Chen, L. / Liu, Y. / Wu, J. / Velazquez-Campoy, A. / Sivaraman, J. / Hew, C.L.
History
DepositionApr 15, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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

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Assembly

Deposited unit
X: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)15,7961
Polymers15,7961
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.066, 41.002, 52.386
Angle α, β, γ (deg.)90.00, 95.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative uncharacterized protein / ORF158L protein


Mass: 15795.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Singapore grouper iridovirus / Gene: ORF158L / Production host: Escherichia coli (E. coli) / References: UniProt: Q5YFA7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.03 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 3% glycerol, 18% PEG3350, 0.1M Tris, 0.3M NaAc, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→52 Å / Num. obs: 6586
Reflection shellHighest resolution: 2.2 Å

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.2→29.9 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.881 / SU B: 6.805 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 5 / ESU R: 0.365 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27503 307 4.7 %RANDOM
Rwork0.19743 ---
obs0.20101 6253 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.685 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å2-0 Å2-0.11 Å2
2---0.59 Å20 Å2
3---2.23 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1075 0 0 69 1144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211105
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9121503
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.875132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74723.21456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.69215173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.682157
X-RAY DIFFRACTIONr_chiral_restr0.1020.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02857
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_it0.7181.5661
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39721064
X-RAY DIFFRACTIONr_scbond_it1.9983444
X-RAY DIFFRACTIONr_scangle_it3.4754.5439
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.199→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 23 -
Rwork0.207 454 -
obs--97.55 %

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