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- PDB-2r72: Crystal structure of infectious bursal disease virus VP1 polymera... -

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Basic information

Entry
Database: PDB / ID: 2r72
TitleCrystal structure of infectious bursal disease virus VP1 polymerase, incubated with Mg2+ ion.
ComponentsINFECTIOUS BURSAL DISEASE VIRUS VP1 POLYMERASE
KeywordsTRANSFERASE / IBDV / infectious bursal disease virus / birnavirus / VP1 / polymerase / magnesium / mg
Function / homology
Function and homology information


viral genome replication / virion component / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTP binding
Similarity search - Function
Rna Polymerase Sigma Factor; Chain: A - #80 / RNA-directed RNA polymerase, C-terminal domain superfamily, Avibirnavirus / Infectious bursal virus vp1 polymerase fold / Infectious bursal virus vp1 polymerase domain / Helix Hairpins - #300 / Birnavirus RNA-directed RNA polymerase, palm domain / RNA-directed RNA polymerase, C-terminal, birnavirus / RNA-directed RNA polymerase, thumb domain, birnavirus / RNA-directed RNA polymerase, palm domain superfamily, Birnavirus / RNA-directed RNA polymerase, thumb domain superfamily, Birnavirus ...Rna Polymerase Sigma Factor; Chain: A - #80 / RNA-directed RNA polymerase, C-terminal domain superfamily, Avibirnavirus / Infectious bursal virus vp1 polymerase fold / Infectious bursal virus vp1 polymerase domain / Helix Hairpins - #300 / Birnavirus RNA-directed RNA polymerase, palm domain / RNA-directed RNA polymerase, C-terminal, birnavirus / RNA-directed RNA polymerase, thumb domain, birnavirus / RNA-directed RNA polymerase, palm domain superfamily, Birnavirus / RNA-directed RNA polymerase, thumb domain superfamily, Birnavirus / Birnavirus RNA dependent RNA polymerase (VP1), palm domain / Birnavirus RNA dependent RNA polymerase (VP1), thumb domain / Birnavirus RNA dependent RNA polymerase (VP1), C-terminal / RdRp of Birnaviridae dsRNA viruses catalytic domain profile. / Helix hairpin bin / Rna Polymerase Sigma Factor; Chain: A / Helix Hairpins / Helix non-globular / Special / Helix Hairpins / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA-directed RNA polymerase
Similarity search - Component
Biological speciesInfectious bursal disease virus (Gumboro virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.15 Å
AuthorsGarriga, D. / Navarro, A. / Querol-Audi, J. / Abaitua, F. / Rodriguez, J.F. / Verdaguer, N.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Activation mechanism of a noncanonical RNA-dependent RNA polymerase.
Authors: Garriga, D. / Navarro, A. / Querol-Audi, J. / Abaitua, F. / Rodriguez, J.F. / Verdaguer, N.
History
DepositionSep 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999Sequence The sequence is not available in the UniProt database at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INFECTIOUS BURSAL DISEASE VIRUS VP1 POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7254
Polymers94,6521
Non-polymers733
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.838, 122.838, 354.255
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein INFECTIOUS BURSAL DISEASE VIRUS VP1 POLYMERASE


Mass: 94651.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious bursal disease virus (Gumboro virus)
Genus: Avibirnavirus / Strain: Soroa / Gene: VP1 polymerase (segment B) / Cell (production host): HighFive cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Q6Q5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.08 Å3/Da / Density % sol: 69.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% PEG 3350, 0.4M LiNO3, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 2, 2006
RadiationMonochromator: si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.15→36.664 Å / Num. all: 27660 / Num. obs: 27660 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.15-3.324.20.3561.91675339620.35698.6
3.32-3.526.10.282.52300037470.2898.9
3.52-3.777.30.2023.32596435360.20298.8
3.77-4.077.30.1564.22437133340.15698.9
4.07-4.457.30.1255.12225730620.12598.7
4.45-4.987.20.1046.12012427840.10498.5
4.98-5.757.10.0976.51770224770.09798.1
5.75-7.0470.1036.21484121180.10397.9
7.04-9.966.60.0629.61114516790.06297.6
9.96-36.664.30.05510.341069610.05593.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PUS

2pus


Resolution: 3.15→20 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.894 / SU B: 35.261 / SU ML: 0.277 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.048 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1393 5.1 %RANDOM
Rwork0.209 ---
obs0.211 27545 97.5 %-
all-27545 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.897 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.17 Å20 Å2
2---0.34 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 3.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5915 0 3 3 5921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226053
X-RAY DIFFRACTIONr_angle_refined_deg0.9621.9788231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7165760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26524.286245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.509151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0411533
X-RAY DIFFRACTIONr_chiral_restr0.0650.2920
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024557
X-RAY DIFFRACTIONr_nbd_refined0.1810.22734
X-RAY DIFFRACTIONr_nbtor_refined0.2970.24184
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2123
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0450.23
X-RAY DIFFRACTIONr_mcbond_it0.2791.53909
X-RAY DIFFRACTIONr_mcangle_it0.50426139
X-RAY DIFFRACTIONr_scbond_it0.44732456
X-RAY DIFFRACTIONr_scangle_it0.8074.52092
LS refinement shellResolution: 3.15→3.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 112 -
Rwork0.29 1846 -
all-1958 -
obs--97.95 %
Refinement TLS params.Method: refined / Origin x: -28.7939 Å / Origin y: -36.4306 Å / Origin z: 111.5113 Å
111213212223313233
T-0.1003 Å20.0865 Å20.1587 Å2--0.2445 Å20.1308 Å2---0.1129 Å2
L1.8178 °2-0.6313 °2-1.0612 °2-1.2136 °20.3366 °2--1.4871 °2
S0.071 Å °0.0715 Å °0.1311 Å °-0.2682 Å °-0.0248 Å °-0.2829 Å °-0.194 Å °0.1837 Å °-0.0462 Å °

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