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- PDB-1hqn: THE SELENOMETHIONINE DERIVATIVE OF P3, THE MAJOR COAT PROTEIN OF ... -

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Basic information

Entry
Database: PDB / ID: 1hqn
TitleTHE SELENOMETHIONINE DERIVATIVE OF P3, THE MAJOR COAT PROTEIN OF THE LIPID-CONTAINING BACTERIOPHAGE PRD1.
ComponentsMAJOR CAPSID PROTEIN
KeywordsVIRAL PROTEIN / bacteriophage PRD1 / Coat protein / jelly roll / viral beta barrel
Function / homology
Function and homology information


Viral coat protein p3 / Adenovirus Type 2 Hexon; domain 4 / Bacteriophage PRD1, P3 / Bacteriophage PRD1, P3, N-terminal / P3 major capsid protein / Group II dsDNA virus coat/capsid protein / Jelly Rolls - #20 / Distorted Sandwich / Viral coat protein subunit / Jelly Rolls ...Viral coat protein p3 / Adenovirus Type 2 Hexon; domain 4 / Bacteriophage PRD1, P3 / Bacteriophage PRD1, P3, N-terminal / P3 major capsid protein / Group II dsDNA virus coat/capsid protein / Jelly Rolls - #20 / Distorted Sandwich / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major capsid protein P3
Similarity search - Component
Biological speciesEnterobacteria phage PRD1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsBenson, S.D. / Bamford, J.K.H. / Bamford, D.H. / Burnett, R.M.
Citation
Journal: Acta Crystallogr D Biol Crystallogr / Year: 2002
Title: The X-ray crystal structure of P3, the major coat protein of the lipid-containing bacteriophage PRD1, at 1.65 A resolution.
Authors: Stacy D Benson / Jaana K H Bamford / Dennis H Bamford / Roger M Burnett /
Abstract: P3 has been imaged with X-ray crystallography to reveal a trimeric molecule with strikingly similar characteristics to hexon, the major coat protein of adenovirus. The structure of native P3 has now ...P3 has been imaged with X-ray crystallography to reveal a trimeric molecule with strikingly similar characteristics to hexon, the major coat protein of adenovirus. The structure of native P3 has now been extended to 1.65 A resolution (R(work) = 19.0% and R(free) = 20.8%). The new high-resolution model shows that P3 forms crystals through hydrophobic patches solvated by 2-methyl-2,4-pentanediol molecules. It reveals details of how the molecule's high stability may be achieved through ordered solvent in addition to intra- and intersubunit interactions. Of particular importance is a 'puddle' at the top of the molecule containing a four-layer deep hydration shell that cross-links a complex structural feature formed by 'trimerization loops'. These loops also link subunits by extending over a neighbor to reach the third subunit in the trimer. As each subunit has two eight-stranded viral jelly rolls, the trimer has a pseudo-hexagonal shape to allow close packing in its 240 hexavalent capsid positions. Flexible regions in P3 facilitate these interactions within the capsid and with the underlying membrane. A selenometh-ionine P3 derivative, with which the structure was solved, has been refined to 2.2 A resolution (R(work) = 20.1% and R(free) = 22.8%). The derivatized molecule is essentially unchanged, although synchrotron radiation has the curious effect of causing it to rotate about its threefold axis. P3 is a second example of a trimeric 'double-barrel' protein that forms a stable building block with optimal shape for constructing a large icosahedral viral capsid. A major difference is that hexon has long variable loops that distinguish different adenovirus species. The short loops in P3 and the severe constraints of its various interactions explain why the PRD1 family has highly conserved coat proteins.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures
Authors: Benson, S.D. / Bamford, J.K.H. / Bamford, D.H. / Burnett, R.M.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of the major coat protein of PRD1, a bacteriophage with an internal membrane
Authors: Stewart, P.L. / Ghosh, S. / Bamford, D.H. / Burnett, R.M.
#3: Journal: Virology / Year: 1990
Title: Capsomer proteins of bacteriophage PRD1, a bacterial virus with a membrane
Authors: Bamford, J.K.H. / Bamford, D.H.
#4: Journal: MOL.THER. / Year: 2000
Title: Type-specific epitope locations revealed by X-ray crystallographic study of adenovirus type 5 hexon
Authors: Rux, J.J. / Burnett, R.M.
History
DepositionDec 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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


Theoretical massNumber of molelcules
Total (without water)130,7423
Polymers130,7423
Non-polymers00
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10090 Å2
ΔGint-56 kcal/mol
Surface area41160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.960, 121.300, 126.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MAJOR CAPSID PROTEIN / PROTEIN P3


Mass: 43580.691 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage PRD1 (virus) / Genus: Tectivirus / Production host: Salmonella typhimurium (bacteria) / References: UniProt: P22535
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 3.46 Å3/Da / Density % sol: 64.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 30% MPD, 0.2 M NACL, 0.1 M SODIUM ACETATE, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
PH range low: 4.3 / PH range high: 4.1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
135 %MPD1reservoir
20.1 Msodium acetate1reservoirpH4.1-4.3
30.2 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9790, 0.9786, 0.9500
DetectorType: BRANDEIS / Detector: CCD / Date: Jun 10, 1997 / Details: mirrors
RadiationMonochromator: SI(III) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97861
30.951
ReflectionResolution: 2.15→100 Å / Num. all: 95154 / Num. obs: 87548 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 6.5 / Net I/σ(I): 22
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 12 / Num. unique all: 11537 / Rsym value: 53.7 / % possible all: 95
Reflection
*PLUS
Lowest resolution: 100 Å

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Processing

Software
NameVersionClassification
PHASESphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→40.63 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 145279.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 978 1.2 %SPHERES
Rwork0.2 ---
all0.2 82178 --
obs0.2 82178 88.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.55 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å20 Å20 Å2
2---0.32 Å20 Å2
3----1.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.2→40.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8537 0 0 437 8974
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.051.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it1.472
X-RAY DIFFRACTIONc_scangle_it2.132.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.248 130 1.7 %
Rwork0.228 7662 -
obs--85.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 35 Å / σ(F): 0 / % reflection Rfree: 1.1 % / Rfactor obs: 0.201 / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73
X-RAY DIFFRACTIONc_mcbond_it1.051.5
X-RAY DIFFRACTIONc_scbond_it1.472
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scangle_it2.132.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.248 / % reflection Rfree: 1.7 % / Rfactor Rwork: 0.228

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