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- PDB-6bl5: Head decoration protein from the hyperthermophilic phage P74-26 -

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Basic information

Entry
Database: PDB / ID: 6bl5
TitleHead decoration protein from the hyperthermophilic phage P74-26
ComponentsHead decoration protein
KeywordsVIRAL PROTEIN / beta-tulip domain / capsid / virion
Function / homologyUncharacterized protein
Function and homology information
Biological speciesThermus virus P74-26
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.69 Å
AuthorsStone, N.P. / Hilbert, B.J. / Hidalgo, D. / Halloran, K.T. / Kelch, B.A.
Funding support United States, 1items
OrganizationGrant numberCountry
The Pew Charitable Trusts United States
CitationJournal: Structure / Year: 2018
Title: A Hyperthermophilic Phage Decoration Protein Suggests Common Evolutionary Origin with Herpesvirus Triplex Proteins and an Anti-CRISPR Protein.
Authors: Stone, N.P. / Hilbert, B.J. / Hidalgo, D. / Halloran, K.T. / Lee, J. / Sontheimer, E.J. / Kelch, B.A.
History
DepositionNov 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Head decoration protein


Theoretical massNumber of molelcules
Total (without water)16,2451
Polymers16,2451
Non-polymers00
Water1,76598
1
A: Head decoration protein

A: Head decoration protein

A: Head decoration protein


Theoretical massNumber of molelcules
Total (without water)48,7363
Polymers48,7363
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.516, 89.516, 31.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Head decoration protein


Mass: 16245.433 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus virus P74-26 / Gene: P74p87 / Production host: Escherichia coli (E. coli) / References: UniProt: A7XXR5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Tris-HCl pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 21, 2017 / Details: Sagitally focusing 2nd crystal
RadiationMonochromator: Si Rosenbaum-Rock double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.69→25.841 Å / Num. obs: 16355 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.023 / Rrim(I) all: 0.062 / Net I/σ(I): 14.3
Reflection shellResolution: 1.69→1.74 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1344 / CC1/2: 0.81 / Rpim(I) all: 0.328 / Rrim(I) all: 0.888 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-3000data collection
HKL-3000v703xdata scaling
Cootv0.8.8model building
AutoSolphasing
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.69→25.841 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.99
RfactorNum. reflection% reflection
Rfree0.2126 1637 10.01 %
Rwork0.1787 --
obs0.1821 16355 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.69→25.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1008 0 0 98 1106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011046
X-RAY DIFFRACTIONf_angle_d1.0461439
X-RAY DIFFRACTIONf_dihedral_angle_d13.775614
X-RAY DIFFRACTIONf_chiral_restr0.066153
X-RAY DIFFRACTIONf_plane_restr0.008192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6904-1.74010.29331340.2691210X-RAY DIFFRACTION100
1.7401-1.79620.30391340.25831212X-RAY DIFFRACTION100
1.7962-1.86040.28851420.24951217X-RAY DIFFRACTION100
1.8604-1.93490.271320.2261209X-RAY DIFFRACTION100
1.9349-2.02290.2951360.23331211X-RAY DIFFRACTION100
2.0229-2.12950.25231350.20221224X-RAY DIFFRACTION100
2.1295-2.26290.22831380.19881220X-RAY DIFFRACTION100
2.2629-2.43750.2381340.1961228X-RAY DIFFRACTION100
2.4375-2.68250.25781350.18971223X-RAY DIFFRACTION100
2.6825-3.07020.20911410.18511232X-RAY DIFFRACTION100
3.0702-3.8660.1891360.16531253X-RAY DIFFRACTION100
3.866-25.84410.16541400.14251279X-RAY DIFFRACTION99

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