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- PDB-4dox: Crystal Structure of Papaya mosaic virus capsid protein -

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Basic information

Entry
Database: PDB / ID: 4dox
TitleCrystal Structure of Papaya mosaic virus capsid protein
ComponentsCoat protein
KeywordsVIRAL PROTEIN / all helix capsid protein / virus capsid structure
Function / homologyPotexviruses and carlaviruses coat protein signature. / Potex/carlavirus coat protein / Viral coat protein / helical viral capsid / viral capsid / structural molecule activity / Coat protein / Coat protein
Function and homology information
Biological speciesPapaya mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.7 Å
AuthorsWang, T. / Li, H.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystal structure of the coat protein of the flexible filamentous papaya mosaic virus.
Authors: Yang, S. / Wang, T. / Bohon, J. / Gagne, N. / Bolduc, M. / Leclerc, D. / Li, H.
History
DepositionFeb 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Oct 8, 2014Group: Structure summary
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coat protein
B: Coat protein


Theoretical massNumber of molelcules
Total (without water)48,7932
Polymers48,7932
Non-polymers00
Water2,756153
1
A: Coat protein


Theoretical massNumber of molelcules
Total (without water)24,3961
Polymers24,3961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Coat protein


Theoretical massNumber of molelcules
Total (without water)24,3961
Polymers24,3961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.943, 72.943, 133.325
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A7 - 170
2116B7 - 170

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Components

#1: Protein Coat protein


Mass: 24396.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PapMV CP (6-215) was constructed into pET-3d vector and An Ala was used to accommodate cloning with NcoI site
Source: (gene. exp.) Papaya mosaic virus / Gene: PapMVgp5 / Plasmid: pET-3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: A2IAW7, UniProt: P16596*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE SEQUENCE HAS BEEN VERIFIED AND THOSE INDICATED IN REMARK 999 APPEAR TO BE ...AUTHORS STATE THAT THE SEQUENCE HAS BEEN VERIFIED AND THOSE INDICATED IN REMARK 999 APPEAR TO BE NATURAL MUTATIONS

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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: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.6
Details: 100 mM Hepes, 9% PEG 6000, pH 7.6, VAPOR DIFFUSION, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.1
SYNCHROTRONNSLS X2521.0082
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 10, 2011
ADSC QUANTUM 3152CCDFeb 10, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.00821
ReflectionResolution: 2.7→45 Å / Num. all: 11087 / Num. obs: 11047 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Rmerge(I) obs: 0.129 / Rsym value: 0.109 / Net I/σ(I): 16.7
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obsMean I/σ(I) obsRsym value
7.32-501,2100
5.81-7.321,2100
4.62-5.081,2100
3.52-3.661,2100
2.75-2.81,2100
2.7-2.758.31,2990.4464.20.414

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.895 / SU B: 21.929 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 5.578 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22848 529 4.8 %RANDOM
Rwork0.16838 ---
obs0.17117 10502 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.274 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20.4 Å2-0 Å2
2--0.81 Å2-0 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 0 153 2621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222524
X-RAY DIFFRACTIONr_angle_refined_deg1.711.9653444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5575326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64424.89494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.57915400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.661510
X-RAY DIFFRACTIONr_chiral_restr0.1110.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0221898
X-RAY DIFFRACTIONr_mcbond_it0.9441.51652
X-RAY DIFFRACTIONr_mcangle_it1.79122680
X-RAY DIFFRACTIONr_scbond_it2.4113872
X-RAY DIFFRACTIONr_scangle_it4.1124.5764
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1234 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.325
LOOSE THERMAL2.1510
LS refinement shellResolution: 2.699→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 33 -
Rwork0.229 749 -
obs--99.49 %
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)
10.18890.03590.03740.85850.40430.9218-0.0468-0.00930.04250.0565-0.00660.04470.08170.08060.05340.0824-0.00020.03280.1187-0.01420.1057-21.6423.861-6.109
20.4162-0.20370.01111.3427-0.87010.9898-0.02760.00880.0937-0.0934-0.0078-0.0540.145-0.10880.03540.0924-0.01440.02840.0869-0.00010.1019-50.971-0.70610.2
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 170
2X-RAY DIFFRACTION2B7 - 170

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