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- PDB-2w4b: Epstein-Barr virus alkaline nuclease D203S mutant -

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Basic information

Entry
Database: PDB / ID: 2w4b
TitleEpstein-Barr virus alkaline nuclease D203S mutant
ComponentsALKALINE EXONUCLEASE
KeywordsHYDROLASE / EXONUCLEASE / ENDONUCLEASE / GAMMA-HERPESVIRUS / EBV / BGLF5 / DNASE / NUCLEASE / HERPESVIRUS / EPSTEIN-BARR VIRUS
Function / homology
Function and homology information


symbiont-mediated suppression of host antigen processing and presentation / exonuclease activity / endonuclease activity / symbiont-mediated degradation of host mRNA / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / host cell nucleus / DNA binding / RNA binding
Similarity search - Function
Herpesvirus alkaline exonuclease, N-terminal domain / Alphaherpesvirus alkaline exonuclease / Viral alkaline exonuclease / Viral alkaline exonuclease / Restriction endonuclease type II-like / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Shutoff alkaline exonuclease
Similarity search - Component
Biological speciesHUMAN HERPESVIRUS 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBuisson, M. / Geoui, T. / Flot, D. / Tarbouriech, N. / Burmeister, W.P.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: A Bridge Crosses the Active Site Canyon of the Epstein-Barr Virus Nuclease with DNase and Rnase Activity.
Authors: Buisson, M. / Geoui, T. / Flot, D. / Tarbouriech, N. / Ressing, M.E. / Wiertz, E.J. / Burmeister, W.P.
History
DepositionNov 24, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALKALINE EXONUCLEASE
B: ALKALINE EXONUCLEASE


Theoretical massNumber of molelcules
Total (without water)105,3882
Polymers105,3882
Non-polymers00
Water00
1
A: ALKALINE EXONUCLEASE


Theoretical massNumber of molelcules
Total (without water)52,6941
Polymers52,6941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ALKALINE EXONUCLEASE


Theoretical massNumber of molelcules
Total (without water)52,6941
Polymers52,6941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)87.510, 63.787, 114.131
Angle α, β, γ (deg.)90.00, 93.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A7 - 462
2111B7 - 462

NCS oper: (Code: given
Matrix: (-0.551, 0.092, -0.83), (0.086, 0.995, 0.054), (0.83, -0.042, -0.556)
Vector: 70.37247, 11.17409, -2.5356)

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Components

#1: Protein ALKALINE EXONUCLEASE / NUCLEASE


Mass: 52693.773 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN HERPESVIRUS 4 (Epstein-Barr virus)
Strain: B95-8 / Plasmid: PFASTBAC HTB / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper)
References: UniProt: P03217, Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 203 TO SER ENGINEERED RESIDUE IN CHAIN B, ASP 203 TO SER
Sequence detailsD203S MUTANT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 7.5
Details: PROTEIN AT 4.5 MG/ML IN 250 MM NACL, 20MM TRIS PH 7.5, RESERVOIR: 10 MM DTT, 10 MM MGCL2, 0.1M HEPES PH 7.0, 1.5% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 23, 2007 / Details: MIRRORS
RadiationMonochromator: CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.5→29.99 Å / Num. obs: 13276 / % possible obs: 86 % / Observed criterion σ(I): 0 / Redundancy: 1.92 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.53
Reflection shellResolution: 3.5→3.53 Å / Redundancy: 1.87 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.02 / % possible all: 88.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0038refinement
MOSFLMdata reduction
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W45

2w45


Resolution: 3.5→31.19 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.837 / SU B: 27.406 / SU ML: 0.429 / Cross valid method: THROUGHOUT / ESU R Free: 0.708 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2555 699 5.1 %RANDOM
Rwork0.18974 ---
obs0.19312 12972 84.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.332 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å2-0.96 Å2
2--1.08 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 3.5→31.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7041 0 0 0 7041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0227209
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.9719780
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2065887
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06523.156320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.834151200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.751557
X-RAY DIFFRACTIONr_chiral_restr0.1220.21080
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215500
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_it0.7571.54461
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47227249
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.80132748
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3284.52531
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3393 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.090.05
2Btight positional0.090.05
1Atight thermal0.20.5
2Btight thermal0.20.5
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 49 -
Rwork0.239 922 -
obs--84.36 %

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