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- PDB-2oa5: Crystal structure of ORF52 from Murid herpesvirus (MUHV-4) (Murin... -

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Basic information

Entry
Database: PDB / ID: 2oa5
TitleCrystal structure of ORF52 from Murid herpesvirus (MUHV-4) (Murine gammaherpesvirus 68) at 2.1 A resolution. Northeast Structural Genomics Consortium target MHR28B.
ComponentsHypothetical protein BQLF2Hypothesis
KeywordsSTRUCTURAL PROTEIN / MhR28B / NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyHerpesvirus BLRF2 / Herpesvirus BLRF2 protein / YejL-like / YejL-like / Orthogonal Bundle / Mainly Alpha / 52 protein
Function and homology information
Biological speciesMurid herpesvirus 4 (Murine herpesvirus 68)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBenach, J. / Chen, Y. / Seetharaman, J. / Janjua, H. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Ho, C.K. / Acton, T.B. / Montelione, G.T. ...Benach, J. / Chen, Y. / Seetharaman, J. / Janjua, H. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Ho, C.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural and functional studies of the abundant tegument protein ORF52 from murine gammaherpesvirus 68.
Authors: Benach, J. / Wang, L. / Chen, Y. / Ho, C.K. / Lee, S. / Seetharaman, J. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Deng, H. / Sun, R. / Tong, L.
History
DepositionDec 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein BQLF2
B: Hypothetical protein BQLF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8334
Polymers25,0362
Non-polymers7972
Water3,567198
1
A: Hypothetical protein BQLF2
B: Hypothetical protein BQLF2
hetero molecules

A: Hypothetical protein BQLF2
B: Hypothetical protein BQLF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6658
Polymers50,0714
Non-polymers1,5944
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area17470 Å2
ΔGint-66 kcal/mol
Surface area17890 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.462, 49.393, 56.379
Angle α, β, γ (deg.)90.00, 111.88, 90.00
Int Tables number5
Space group name H-MC121
DetailsAU contains the biological assembly (dimer). A tetramer might be another viable biological assembly. Static light scattering shows a tetramer.

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Components

#1: Protein Hypothetical protein BQLF2 / Hypothesis / Hypothetical protein GAMMAHV.ORF52 / 52


Mass: 12517.789 Da / Num. of mol.: 2 / Fragment: residues 1-102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid herpesvirus 4 (Murine herpesvirus 68)
Genus: Rhadinovirus / Strain: WUMS / Gene: BQLF2, 52, GAMMAHV.ORF52 / Plasmid: pet21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: P88989
#2: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 398.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 80% PEG 400, 100MM MOPS, 100MM NANO3, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97903
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 9, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionRedundancy: 7.1 % / Av σ(I) over netI: 18.8 / Number: 97958 / Rmerge(I) obs: 0.064 / Χ2: 1.95 / D res high: 2.1 Å / D res low: 20 Å / Num. obs: 13827 / % possible obs: 98.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.512099.910.0513.0666.6
3.594.5110010.0492.8477.2
3.133.5910010.0622.7057.4
2.853.1310010.082.3327.5
2.642.8510010.1091.9117.6
2.492.6410010.1221.5477.6
2.362.4910010.1541.2617.6
2.262.3610010.2141.1087.5
2.172.2696.910.3171.3126.2
2.12.1786.710.3531.0025.2
ReflectionResolution: 2.1→20 Å / Num. obs: 13827 / % possible obs: 98.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.175.20.353186.7
2.17-2.266.20.317196.9
2.26-2.367.50.2141100
2.36-2.497.60.1541100
2.49-2.647.60.1221100
2.64-2.857.60.1091100
2.85-3.137.50.081100
3.13-3.597.40.0621100
3.59-4.517.20.0491100
4.51-206.60.051199.9

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Phasing

Phasing MRRfactor: 39 / Cor.coef. Fo:Fc: 71.45
Highest resolutionLowest resolution
Rotation2.5 Å20 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
COMO1.2phasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / σ(F): 752 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.241 1295 9.2 %
Rwork0.215 --
obs0.215 12751 90.6 %
Solvent computationBsol: 73.98 Å2
Displacement parametersBiso mean: 50.07 Å2
Baniso -1Baniso -2Baniso -3
1-8.606 Å20 Å21.1655 Å2
2---13.391 Å20 Å2
3---4.785 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1470 0 54 198 1722
LS refinement shellResolution: 2.1→2.13 Å / Total num. of bins used: 25 /
RfactorNum. reflection
Rfree0.2664 35
Rwork0.2376 276
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PAR
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3PE5.PAR

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