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- PDB-3fbm: D431N Mutant VP2 Protein of Infectious Bursal Disease Virus; Deri... -

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Basic information

Entry
Database: PDB / ID: 3fbm
TitleD431N Mutant VP2 Protein of Infectious Bursal Disease Virus; Derived T=1 Particles
ComponentsPolyprotein
KeywordsVIRUS / capsid protein / autoproteolytic activity / capsid maturation / virus assembly / IBDV
Function / homology
Function and homology information


T=13 icosahedral viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / host cell cytoplasm / structural molecule activity / proteolysis / identical protein binding / metal ion binding
Similarity search - Function
icosahedral virus / Birnavirus VP3, domain 2 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. ...icosahedral virus / Birnavirus VP3, domain 2 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Structural polyprotein / Structural polyprotein
Similarity search - Component
Biological speciesAvian Infectious bursal disease virus (Gumboro virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsIrigoyen, N. / Garriga, D. / Navarro, A. / Verdaguer, N. / Rodriguez, J.F. / Caston, J.R.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Autoproteolytic Activity Derived from the Infectious Bursal Disease Virus Capsid Protein
Authors: Irigoyen, N. / Garriga, D. / Navarro, A. / Verdaguer, N. / Rodriguez, J.F. / Caston, J.R.
History
DepositionNov 19, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 30, 2012Group: Other
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5112
Polymers48,4711
Non-polymers401
Water00
1
A: Polyprotein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)2,910,645120
Polymers2,908,24160
Non-polymers2,40560
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Polyprotein
hetero molecules
x 5


  • icosahedral pentamer
  • 243 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)242,55410
Polymers242,3535
Non-polymers2005
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Polyprotein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 291 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)291,06512
Polymers290,8246
Non-polymers2406
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: Polyprotein
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 2.91 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)2,910,645120
Polymers2,908,24160
Non-polymers2,40560
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)326.725, 326.725, 326.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.87622, 0.21497, 0.43131), (0.31192, 0.42925, -0.84761), (-0.36735, 0.87723, 0.30906)-45.71324, 96.78391, 16.06804
3generate(0.8866, -0.02695, -0.46175), (-0.42026, -0.4639, -0.77985), (-0.19319, 0.88548, -0.42262)52.52343, 232.55489, 64.07681
4generate(0.67518, 0.65961, 0.33022), (0.71941, -0.48988, -0.49241), (-0.16303, 0.57003, -0.80529)-58.18129, 110.45954, 122.5597
5generate(0.25627, 0.93697, -0.2375), (-0.04141, -0.23484, -0.97115), (-0.96572, 0.25871, -0.02138)3.94061, 195.4626, 150.46658
6generate(0.8839, -0.42591, -0.19318), (-0.02802, -0.46055, 0.88719), (-0.46683, -0.77878, -0.41902)63.85094, 52.25726, 232.38937
7generate(-0.49468, 0.71484, -0.49426), (-0.80209, -0.15659, 0.5763), (0.33457, 0.68153, 0.65084)110.9015, 120.3618, -57.57063
8generate(0.32525, -0.75802, -0.56535), (-0.7585, -0.56615, 0.32271), (-0.5647, 0.32386, -0.7591)174.02548, 174.41431, 175.11038
9generate(-0.12043, 0.25779, -0.95867), (-0.64511, -0.75432, -0.1218), (-0.75454, 0.60378, 0.25715)158.98862, 219.99136, 78.01762
10generate(0.67639, 0.71767, -0.16567), (0.65911, -0.48939, 0.57103), (0.32873, -0.49544, -0.80404)-19.94399, 22.64768, 172.35469
11generate(0.43232, 0.87633, 0.21249), (-0.84691, 0.3137, 0.42934), (0.30958, -0.36557, 0.87779)-45.56898, 96.2681, 15.41064
12generate(0.93841, -0.22585, 0.26149), (-0.22576, -0.9737, -0.03077), (0.26156, -0.03016, -0.96472)2.08566, 194.51923, 151.77153
13generate(0.26395, -0.75357, 0.60204), (-0.95741, -0.12894, 0.25835), (-0.11705, -0.64459, -0.75551)77.37345, 159.18491, 220.26677
14generate(0.65492, 0.33331, 0.67822), (-0.49008, -0.49583, 0.71692), (0.57524, -0.8019, -0.16138)-58.5604, 110.40802, 121.60214
15generate(0.57274, 0.65511, -0.49275), (-0.80355, 0.32982, -0.4955), (-0.16209, 0.67974, 0.71532)23.15263, 171.88333, -20.2317
16generate(0.60302, 0.2563, -0.75543), (0.26162, -0.95815, -0.11624), (-0.7536, -0.12754, -0.64484)78.2212, 158.24312, 220.5239
17generate(0.87719, 0.30831, -0.36808), (0.21552, 0.4322, 0.87564), (0.42905, -0.84743, 0.31268)15.93252, -45.68928, 96.54683
18generate(-0.48402, 0.59026, 0.646), (-0.49944, -0.79253, 0.34993), (0.71853, -0.15327, 0.6784)22.43086, 168.6143, -20.70592
19generate(-0.46261, 0.88607, -0.02954), (-0.77796, -0.4217, -0.46578), (-0.42517, -0.19249, 0.88441)52.84395, 232.87601, 63.7467
20generate(-0.22663, 0.2618, 0.93814), (-0.97358, -0.03318, -0.22593), (-0.02802, -0.96455, 0.26241)2.05592, 194.76619, 151.1425

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Components

#1: Protein Polyprotein / VP2 capsid protein


Mass: 48470.676 Da / Num. of mol.: 1 / Mutation: D431N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Avian Infectious bursal disease virus (Gumboro virus)
Strain: SOROA / Gene: CAPSID PROTEIN VP2 / Plasmid: PESC-URA / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): YPH499 / References: UniProt: Q9WI42, UniProt: P61825*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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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 % sol: 50.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 14-17% PEG 4000, 0.1M TRIS pH 9.0, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Jun 27, 2007
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: 3.1→50 Å / Num. all: 208686 / Num. obs: 206393 / % possible obs: 99 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.3 % / Rsym value: 0.12 / Net I/σ(I): 9.3
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.9 / % possible all: 95.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC(Rigid Body)refinement
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
REFMAC(Rigid Body)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GSY

2gsy


Resolution: 3.1→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 16641454.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 10000 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.291 9151 4.9 %RANDOM
Rwork0.294 ---
all0.301 189714 --
obs0.294 187105 90 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.265255 e/Å3
Displacement parametersBiso mean: 35.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.51 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3209 0 1 0 3210
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.682
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.992.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 1238 4.7 %
Rwork0.346 25012 -
obs--76.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top

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