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- PDB-2wlp: Sesbania mosaic virus capsid protein dimer mutant (rCP-DEL-N65-W170K) -

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Basic information

Entry
Database: PDB / ID: 2wlp
TitleSesbania mosaic virus capsid protein dimer mutant (rCP-DEL-N65-W170K)
ComponentsCOAT PROTEIN
KeywordsVIRAL PROTEIN / PROTEIN-PROTEIN INTERACTIONS / CA2+ / VIRUS CAPSID / VIRUS ASSEMBLY / VIRUS STABILITY
Function / homology
Function and homology information


viral capsid / structural molecule activity / metal ion binding
Similarity search - Function
Plant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSESBANIA MOSAIC VIRUS
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsAnju, P. / Subashchandrabose, C. / Satheshkumar, P.S. / Savithri, H.S. / Murthy, M.R.N.
CitationJournal: Virology / Year: 2009
Title: A Single Point Mutation Disrupts the Capsid Assembly in Sesbania Mosaic Virus Resulting in a Stable Isolated Dimer.
Authors: Pappachan, A. / Chinnathambi, S. / Satheshkumar, P.S. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionJun 24, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 17, 2013Group: Database references
Revision 1.3Feb 25, 2015Group: Source and taxonomy
Revision 1.4Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Oct 9, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns / reflns_shell
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf ..._exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.6Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

Downloads & links

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Assembly

Deposited unit
A: COAT PROTEIN
B: COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)42,8282
Polymers42,8282
Non-polymers00
Water84747
1
A: COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,4141
Polymers21,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,4141
Polymers21,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)35.880, 41.950, 68.650
Angle α, β, γ (deg.)81.07, 75.00, 84.25
Int Tables number1
Space group name H-MP1

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Components

#1: Protein COAT PROTEIN


Mass: 21414.184 Da / Num. of mol.: 2 / Fragment: RESIDUES 66-268 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SESBANIA MOSAIC VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-PSBET A / References: UniProt: Q9EB06
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TRP 170 TO LYS ENGINEERED RESIDUE IN CHAIN B, TRP 170 TO LYS

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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: 1.97 Å3/Da / Density % sol: 37.54 % / Description: NONE
Crystal growMethod: microbatch / pH: 6.5 / Details: 0.1 M BIS TRIS (PH 6.5) AND 28% PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→41.34 Å / Num. obs: 10322 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 9.9
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.2 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.4.0069refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VAK

1vak


Resolution: 2.65→65.65 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.861 / SU B: 41.705 / SU ML: 0.417 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29399 493 4.8 %RANDOM
Rwork0.22055 ---
obs0.22403 9828 93.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.912 Å2
Baniso -1Baniso -2Baniso -3
1-2.64 Å24.21 Å2-2.12 Å2
2---0.7 Å2-2.59 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.65→65.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 0 47 2816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222831
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9553878
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1855375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47423.33384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.37715419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.321159
X-RAY DIFFRACTIONr_chiral_restr0.0870.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212057
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_it0.4331.51873
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.78523022
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0093958
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6454.5855
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: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 33 -
Rwork0.307 707 -
obs--91.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2543-0.95130.62024.83583.17096.1668-0.373-0.24770.18960.5280.04740.33820.0482-0.10770.3256-0.192-0.06620.1108-0.12690.0458-0.1083-6.2895-6.237422.4285
21.0386-0.984-0.45973.22130.86430.92230.42630.2054-0.2912-0.6704-0.50290.15950.19280.15740.0766-0.04230.0535-0.018-0.04270.0083-0.08143.52528.4768-7.3499
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A73 - 264
2X-RAY DIFFRACTION2B73 - 264

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