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- PDB-3qpr: HK97 Prohead I encapsidating inactive virally encoded protease -

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Basic information

Entry
Database: PDB / ID: 3qpr
TitleHK97 Prohead I encapsidating inactive virally encoded protease
ComponentsMajor capsid protein
KeywordsVIRUS / Virus Procapsid particles
Function / homologyPhage capsid / Phage capsid family / viral procapsid maturation / T=7 icosahedral viral capsid / viral capsid / identical protein binding / Major capsid protein
Function and homology information
Biological speciesEnterobacteria phage HK97 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.2 Å
AuthorsHuang, R.K. / Khayat, R. / Lee, K.K. / Gertsman, I. / Duda, R.L. / Hendrix, R.W. / Johnson, J.E.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Prohead-I structure of bacteriophage HK97: implications for scaffold-mediated control of particle assembly and maturation.
Authors: Huang, R.K. / Khayat, R. / Lee, K.K. / Gertsman, I. / Duda, R.L. / Hendrix, R.W. / Johnson, J.E.
History
DepositionFeb 14, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionMar 30, 2011ID: 3P8Q
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Derived calculations
Revision 1.3Jan 30, 2013Group: Other
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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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
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)296,0057
Polymers296,0057
Non-polymers00
Water0
1
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)17,760,310420
Polymers17,760,310420
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
x 5


  • icosahedral pentamer
  • 1.48 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,480,02635
Polymers1,480,02635
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
x 6


  • icosahedral 23 hexamer
  • 1.78 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,776,03142
Polymers1,776,03142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
x 5


  • crystal asymmetric unit, crystal frame
  • 1.48 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,480,02635
Polymers1,480,02635
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)560.120, 560.120, 560.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699)
3generate(-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5)
4generate(-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5)
5generate(0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699)
DetailsT=7 Laevo

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Components

#1: Protein
Major capsid protein / Gp5 / Head protein


Mass: 42286.453 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage HK97 (virus) / Gene: 5 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) Plys S / References: UniProt: P49861
Sequence detailsTHE FULL LENGTH PROTEIN WAS CRYSTALLIZED. THERE SHOULD BE A MAIN-CHAIN BREAK BETWEEN A160 AND P170, ...THE FULL LENGTH PROTEIN WAS CRYSTALLIZED. THERE SHOULD BE A MAIN-CHAIN BREAK BETWEEN A160 AND P170, WHERE THE ACTUAL SEQUENCE WAS MODELED AS A SHORTER CONTINUOUS LOOP.

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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: 4.95 Å3/Da / Density % sol: 75.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 4.0% PEG 4000, 0.2M sodium acetate pH 4.6, 0.3M calcium chloride, 15% glycerol, 0.1M sarcosine, 6% n-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.99 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 23, 2008
RadiationMonochromator: 0.99 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 5.2→45 Å / Num. obs: 86130 / % possible obs: 77.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.08
Reflection shellResolution: 5.2→5.29 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3072 / % possible all: 3.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
RAVEmodel building
CNS1.1refinement
HKL-2000data reduction
SCALAdata scaling
RAVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 5.2→45 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.467 9329 random
Rwork0.461 --
all0.461 86130 -
obs0.461 84108 -
Refinement stepCycle: LAST / Resolution: 5.2→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8654 0 0 0 8654

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