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- PDB-4agj: Crystal structure of the capsid protein (110-267) from Aura virus... -

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Basic information

Entry
Database: PDB / ID: 4agj
TitleCrystal structure of the capsid protein (110-267) from Aura virus in complex with dioxane
ComponentsCAPSID PROTEIN
KeywordsHYDROLASE / VIRAL PROTEIN / DIOXANE
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / membrane
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Structural polyprotein
Similarity search - Component
Biological speciesAURA VIRUS
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsAggarwal, M. / Kumar, P. / Tomar, S.
Citation
Journal: Plos One / Year: 2012
Title: Crystal Structure of Aura Virus Capsid Protease and its Complex with Dioxane: New Insights Into Capsid-Glycoprotein Molecular Contacts.
Authors: Aggarwal, M. / Tapas, S. / Preeti / Siwach, A. / Kumar, P. / Kuhn, R.J. / Tomar, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization, High-Resolution Data Collection and Preliminary Crystallographic Analysis of Aura Virus Capsid Protease and its Complex with Dioxane.
Authors: Aggarwal, M. / Dhindwal, S. / Pratap, S. / Kuhn, R.J. / Kumar, P. / Tomar, S.
History
DepositionJan 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0972
Polymers17,0091
Non-polymers881
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.434, 35.425, 49.171
Angle α, β, γ (deg.)90.00, 101.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CAPSID PROTEIN / COAT PROTEIN / C


Mass: 17009.230 Da / Num. of mol.: 1 / Fragment: RESIDUES 110-267
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AURA VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q86925, togavirin
#2: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSOME RESIDUES ARE FOUND TO BE DIFFERENT IN OUR DATA

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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: 1.99 Å3/Da / Density % sol: 38.31 % / Description: NONE
Crystal growDetails: BIS-TRIS AND POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 7989 / % possible obs: 83.9 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.34
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2 / % possible all: 33.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KXA

1kxa


Resolution: 1.98→48.17 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.617 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26757 388 4.9 %RANDOM
Rwork0.17906 ---
obs0.18319 7600 83.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.728 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å2-1.3 Å2
2--0.72 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.98→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1152 0 6 102 1260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021187
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9491603
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8275151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.00524.04347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58515193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.726154
X-RAY DIFFRACTIONr_chiral_restr0.1130.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021895
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 1.978→2.029 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.725 7 -
Rwork0.318 128 -
obs--20.12 %
Refinement TLS params.Method: refined / Origin x: -23.8634 Å / Origin y: 0.5096 Å / Origin z: -11.3348 Å
111213212223313233
T0.0313 Å2-0.0177 Å2-0.027 Å2-0.0377 Å20.0058 Å2--0.0412 Å2
L1.0915 °2-0.0051 °20.8551 °2-0.6379 °20.011 °2--1.6008 °2
S-0.0677 Å °0.0878 Å °0.0723 Å °0.05 Å °0.0133 Å °-0.051 Å °-0.0858 Å °0.1949 Å °0.0544 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A136 - 210
2X-RAY DIFFRACTION1A211 - 267

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