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- PDB-3e8k: Crystal structure of HK97 Prohead II -

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Basic information

Entry
Database: PDB / ID: 3e8k
TitleCrystal structure of HK97 Prohead II
ComponentsMajor capsid protein
KeywordsVIRUS / HK97 capsid fold / Capsid protein / Virion
Function / homology
Function and homology information


viral procapsid maturation / T=7 icosahedral viral capsid / viral capsid / identical protein binding
Similarity search - Function
Major capsid protein gp5 / hypothetical protein PF0899 domain / Major capsid protein gp5 fold / hypothetical protein PF0899 fold / Phage capsid / Phage capsid family / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Major capsid protein
Similarity search - Component
Biological speciesEnterobacteria phage HK97 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.65 Å
AuthorsGertsman, I. / Speir, J. / Johnson, J.E.
CitationJournal: Nature / Year: 2009
Title: An unexpected twist in viral capsid maturation.
Authors: Gertsman, I. / Gan, L. / Guttman, M. / Lee, K. / Speir, J.A. / Duda, R.L. / Hendrix, R.W. / Komives, E.A. / Johnson, J.E.
History
DepositionAug 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.5May 11, 2022Group: Derived calculations / Other / Refinement description
Category: cell / pdbx_struct_assembly ...cell / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_ncs_oper
Item: _cell.Z_PDB / _pdbx_struct_assembly.oligomeric_count ..._cell.Z_PDB / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 1.6Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)208,1697
Polymers208,1697
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)12,490,112420
Polymers12,490,112420
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
  • 1.04 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,040,84335
Polymers1,040,84335
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
  • 1.25 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,249,01142
Polymers1,249,01142
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 15


  • crystal asymmetric unit, crystal frame
  • 3.12 MDa, 105 polymers
Theoretical massNumber of molelcules
Total (without water)3,122,528105
Polymers3,122,528105
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)553.033, 574.390, 587.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
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)
6generate(1), (1), (1)
7generate(-0.5, 0.30901699, 0.80901699), (0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699)
8generate(-0.30901699, 0.80901699, 0.5), (-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699)
9generate(0.30901699, 0.80901699, 0.5), (-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699)
10generate(0.5, 0.30901699, 0.80901699), (0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699)
11generate(1), (1), (1)
12generate(0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699), (0.30901699, -0.80901699, 0.5)
13generate(0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5), (-0.80901699, -0.5, 0.30901699)
14generate(-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5), (-0.80901699, 0.5, -0.30901699)
15generate(-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699), (0.30901699, 0.80901699, -0.5)

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Components

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


Mass: 29738.361 Da / Num. of mol.: 7 / Mutation: W336F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage HK97 (virus) / Gene: 5 / Cell line (production host): BL21-DE3(plys-S) / Production host: Escherichia coli (E. coli) / References: UniProt: P49861
Sequence detailsTHE FIRST 103 RESIDUES ARE CLEAVED. THE SEQUENCE OF PROHEAD II BEGINS AT RESIDUE 104. THERE IS ...THE FIRST 103 RESIDUES ARE CLEAVED. THE SEQUENCE OF PROHEAD II BEGINS AT RESIDUE 104. THERE IS DYNAMICS IN THE N-TERMINUS REGION THEREFORE SOME N-TERMINAL RESIDUES COULD NOT BE MODELED IN THE CRYSTAL STRUCTURE. THE CONSTRUCT WAS ALSO TRUNCATED BETWEEN RESIDUE 159-171 AND REPLACED BY THE LINKER APGD.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 29

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Sample preparation

CrystalDensity Matthews: 7.48 Å3/Da / Density % sol: 83.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100mM CHES pH 9.0, 200mM Manganese Chloride, 2.7% PEG 4k, 200mM NDSB-211(in drop only), VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12951
22951
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-C10.9
SYNCHROTRONAPS 23-ID-D20.83
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 18, 2008
ADSC QUANTUM 3152CCDApr 17, 2008
Radiation
IDProtocolScattering typeWavelength-IDMonochromatic (M) / Laue (L)
1SINGLE WAVELENGTHx-ray1
2SINGLE WAVELENGTHx-ray2M
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.831
ReflectionResolution: 3.65→35 Å / Num. all: 656590 / Num. obs: 656590 / Observed criterion σ(I): 0 / Redundancy: 1 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.184 / Rsym value: 0.184 / Net I/σ(I): 2.5
Reflection shellResolution: 3.65→3.74 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 1.4 / Num. unique all: 11086 / Rsym value: 0.431 / % possible all: 14.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
DENZOdata reduction
SCALEPACKdata scaling
RAVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Prohead II 12A Cryo-EM model and PII 5.2A crystal structure

Resolution: 3.65→35 Å / Occupancy max: 1 / Occupancy min: 1 / σ(I): 0
Details: cross validation was not used and R-free was not calculated due to the high NCS symmetry (15-fold).
RfactorNum. reflection% reflection
all0.366 656526 -
obs0.365 656526 64.8 %
Displacement parametersBiso max: 82.86 Å2 / Biso mean: 35.6 Å2 / Biso min: 1 Å2
Refinement stepCycle: LAST / Resolution: 3.65→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13590 0 0 0 13590
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.49
LS refinement shellHighest resolution: 3.65 Å
RfactorNum. reflection% reflection
Rwork0.366 --
obs-656590 64.8 %

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