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- PDB-5tip: The Structure of the Major Capsid protein of PBCV-1 -

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Basic information

Entry
Database: PDB / ID: 5tip
TitleThe Structure of the Major Capsid protein of PBCV-1
ComponentsMajor capsid protein
KeywordsVIRAL PROTEIN
Function / homologyMajor capsid protein, C-terminal / Hexon coat protein, subdomain 4 / Group II dsDNA virus coat/capsid protein / Major capsid protein, N-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Major capsid protein N-terminus / viral capsid / structural molecule activity / Major capsid protein
Function and homology information
Specimen sourceParamecium bursaria Chlorella virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2 Å resolution
AuthorsKlose, T. / De Castro, C. / Speciale, I. / Molinaro, A. / Van Etten, J.L. / Rossmann, M.G.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure of the chlorovirus PBCV-1 major capsid glycoprotein determined by combining crystallographic and carbohydrate molecular modeling approaches.
Authors: De Castro, C. / Klose, T. / Speciale, I. / Lanzetta, R. / Molinaro, A. / Van Etten, J.L. / Rossmann, M.G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 3, 2016 / Release: Oct 18, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 18, 2017Structure modelrepositoryInitial release
1.1Dec 20, 2017Structure modelDatabase referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
1.2Jan 3, 2018Structure modelDatabase referencescitation_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
1.3Jan 17, 2018Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,248110
Polyers192,2744
Non-polymers17,974106
Water20,8791159
1
A: Major capsid protein
hetero molecules

A: Major capsid protein
hetero molecules

A: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,50087
Polyers144,2053
Non-polymers14,29484
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area (Å2)34560
ΔGint (kcal/M)-4
Surface area (Å2)46300
MethodPISA
2
B: Major capsid protein
hetero molecules

B: Major capsid protein
hetero molecules

B: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,38281
Polyers144,2053
Non-polymers13,17778
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area (Å2)33870
ΔGint (kcal/M)-13
Surface area (Å2)45420
MethodPISA
3
C: Major capsid protein
hetero molecules

C: Major capsid protein
hetero molecules

C: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,93878
Polyers144,2053
Non-polymers12,73375
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area (Å2)33880
ΔGint (kcal/M)-12
Surface area (Å2)45060
MethodPISA
4
D: Major capsid protein
hetero molecules

D: Major capsid protein
hetero molecules

D: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,92384
Polyers144,2053
Non-polymers13,71881
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area (Å2)34590
ΔGint (kcal/M)-10
Surface area (Å2)45830
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)188.792, 188.792, 188.792
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP 21 3

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Components

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Protein/peptide , 1 types, 4 molecules ABCD

#1: Protein/peptide
Major capsid protein / MCP / VP54


Mass: 48068.430 Da / Num. of mol.: 4 / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: P30328

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Non-polymers , 10 types, 1265 molecules

#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 4 / Formula: Hg / Mercury
#3: Chemical
ChemComp-BGC / BETA-D-GLUCOSE


Mass: 180.156 Da / Num. of mol.: 16 / Formula: C6H12O6 / Glucose
#4: Chemical
ChemComp-FUC / ALPHA-L-FUCOSE


Mass: 164.156 Da / Num. of mol.: 15 / Formula: C6H12O5
#5: Chemical...
ChemComp-XYP / BETA-D-XYLOPYRANOSE


Mass: 150.130 Da / Num. of mol.: 24 / Formula: C5H10O5
#6: Chemical
ChemComp-GLA / ALPHA D-GALACTOSE


Mass: 180.156 Da / Num. of mol.: 12 / Formula: C6H12O6
#7: Chemical
ChemComp-XXR / 6-deoxy-alpha-D-mannopyranose / D-Rhamnose


Mass: 164.156 Da / Num. of mol.: 12 / Formula: C6H12O5
#8: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 11 / Formula: C6H12O6
#9: Chemical
ChemComp-RM4 / 6-deoxy-beta-L-mannopyranose


Mass: 164.156 Da / Num. of mol.: 7 / Formula: C6H12O5
#10: Chemical
ChemComp-7CV / 6-deoxy-2,3-di-O-methyl-alpha-L-mannopyranose


Mass: 192.210 Da / Num. of mol.: 5 / Formula: C8H16O5
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1159 / Formula: H2O / Water

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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: 2.92 / Density percent sol: 57.82 %
Crystal growTemp: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 3.4~4.0 M sodium formate, 50 mM Tris, pH 7.5

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 14-BM-C / Synchrotron site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Collection date: Feb 13, 2002
RadiationMonochromator: double crystal Si(111) / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
Reflection twin
Crystal IDIdOperatorDomain IDFraction
11H, K, L10.696
11L, -K, H20.304
ReflectionD resolution high: 2 Å / D resolution low: 100 Å / Number obs: 148902 / Rmerge I obs: 0.132 / Redundancy: 40 % / Percent possible obs: 99
Reflection shellRmerge I obs: 0.532 / Highest resolution: 2 Å / Lowest resolution: 2.07 Å / Percent possible all: 98.8

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Processing

SoftwareName: PHENIX / Version: (1.11.1_2575: ???) / Classification: refinement
RefineR Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 5.6 / Overall phase error: 25.34 / Stereochemistry target values: TWIN_LSQ_F
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.206 / R factor R work: 0.1761 / R factor obs: 0.1831 / Highest resolution: 2 Å / Lowest resolution: 84.43 Å / Number reflection R free: 4236 / Number reflection obs: 139146 / Percent reflection R free: 3.04 / Percent reflection obs: 92.53
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 84.43 Å
Number of atoms included #LASTProtein: 13580 / Nucleic acid: 0 / Ligand: 1049 / Solvent: 1159 / Total: 15788
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415039
X-RAY DIFFRACTIONf_angle_d0.86820675
X-RAY DIFFRACTIONf_dihedral_angle_d11.8205626
X-RAY DIFFRACTIONf_chiral_restr0.4842530
X-RAY DIFFRACTIONf_plane_restr0.0032480
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
2.00010.27880.28462.0345189634085.00
2.03450.26480.26352.0714201650587.00
2.07140.30640.26122.1112207645787.00
2.11120.27130.24912.1542186664888.00
2.15420.30350.24472.2010179651688.00
2.20100.27260.23952.2521218669090.00
2.25210.25080.23352.3083197676890.00
2.30830.24100.22792.3705198677691.00
2.37050.25450.23312.4401207680091.00
2.44010.26360.22332.5186219690892.00
2.51860.23800.22062.6084220692793.00
2.60840.27530.21432.7124223702394.00
2.71240.21830.20552.8354227712695.00
2.83540.21290.18942.9842244715696.00
2.98420.19590.17983.1701215720396.00
3.17010.20920.16353.4131220727496.00
3.41310.15800.14343.7535239723596.00
3.75350.13760.12964.2895201712194.00
4.28950.16840.12635.3776157643384.00
5.37760.20080.177517.3804148509066.00

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