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- PDB-3qc7: The structure of bacteriophage phi29 head fibers has a supercoile... -

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Basic information

Entry
Database: PDB / ID: 3qc7
TitleThe structure of bacteriophage phi29 head fibers has a supercoiled triple repeating helix-turn-helix motif
ComponentsHead fiber protein
KeywordsVIRAL PROTEIN / supercoiled triple repeating helix-turn-helix
Function / homology
Function and homology information


viral capsid, fiber / viral procapsid / symbiont entry into host cell / virion attachment to host cell / identical protein binding
Similarity search - Function
Helix Hairpins - #1630 / Bacteriophage B103, Gp8, head fibre / Head fiber protein / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Capsid fiber protein / Capsid fiber protein
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å
AuthorsXiang, Y. / Rossmann, M.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structure of bacteriophage {phi}29 head fibers has a supercoiled triple repeating helix-turn-helix motif.
Authors: Xiang, Y. / Rossmann, M.G.
History
DepositionJan 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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

Downloads & links

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Assembly

Deposited unit
A: Head fiber protein


Theoretical massNumber of molelcules
Total (without water)18,9231
Polymers18,9231
Non-polymers00
Water3,225179
1
A: Head fiber protein

A: Head fiber protein

A: Head fiber protein


Theoretical massNumber of molelcules
Total (without water)56,7703
Polymers56,7703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area17320 Å2
ΔGint-152 kcal/mol
Surface area21680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.248, 47.248, 424.752
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Head fiber protein / Late protein GP8.5


Mass: 18923.359 Da / Num. of mol.: 1 / Fragment: gp8.5 fibrous portion (UNP residues 110-280)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus) / Gene: 8.5 / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / References: UniProt: P20344, UniProt: B3VMP4*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: The gp8.5 fragment crystals were grown in 100mM sodium phosphate at pH ~6.8 and 8% w/v PEG 3000. It took about one week for crystals to appear, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.968 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.52→70 Å / Num. all: 28649 / Num. obs: 28649 / % possible obs: 98.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 33.4
Reflection shellResolution: 1.52→1.57 Å / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 4.6 / % possible all: 97.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHARPphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.52→29.47 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.121 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.077
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21833 1442 5 %RANDOM
Rwork0.19424 ---
all0.19542 27206 --
obs0.19542 27206 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.52→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 0 179 1373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221245
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9871705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5185178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.2192845
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9615231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.537153
X-RAY DIFFRACTIONr_chiral_restr0.0830.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021893
X-RAY DIFFRACTIONr_mcbond_it0.8951.5834
X-RAY DIFFRACTIONr_mcangle_it1.64221358
X-RAY DIFFRACTIONr_scbond_it2.6273411
X-RAY DIFFRACTIONr_scangle_it4.3944.5339
LS refinement shellResolution: 1.521→1.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 95 -
Rwork0.255 1886 -
obs--94.92 %

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