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- PDB-2gp1: Bacteriophage HK97 Prohead II crystal structure -

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Basic information

Entry
Database: PDB / ID: 2gp1
TitleBacteriophage HK97 Prohead II crystal structure
ComponentsMajor capsid protein
KeywordsVIRUS / icosahedral Virus
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
AuthorsGertsman, I. / Gan, L. / Johnson, J.E.
CitationJournal: To be Published
Title: Structure and Flexibility of Bacteriophage HK97 Pre-expanded State Prohead II
Authors: Gertsman, I. / Gan, L. / Wikoff, W. / Guttman, M. / Duda, R.L. / Hendrix, R.W. / Komives, E.A. / Johnson, J.E.
History
DepositionApr 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Refinement description / Category: database_2 / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_PDB_matrix / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_ncs_oper
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)215,3597
Polymers215,3597
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)12,921,540420
Polymers12,921,540420
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
  • 1.08 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,076,79535
Polymers1,076,79535
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
  • 1.29 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,292,15442
Polymers1,292,15442
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
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 20


  • crystal asymmetric unit, crystal frame
  • 4.31 MDa, 140 polymers
Theoretical massNumber of molelcules
Total (without water)4,307,180140
Polymers4,307,180140
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)706.940, 706.940, 706.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.34073714, -0.87698289, 0.33882051), (0.93847651, 0.33882034, -0.06680236), (-0.05621475, 0.34073696, 0.93847651)213.9051, -37.60222, -39.83594
3generate(-0.72597275, -0.48051161, 0.49200835), (0.64150401, -0.73099065, 0.23264864), (0.24786297, 0.48452163, 0.83892942)306.26978, 153.06343, -102.05813
4generate(-0.72597286, 0.641504, 0.24786314), (-0.4805116, -0.73099054, 0.48452191), (0.49200807, 0.23264847, 0.83892942)149.44919, 308.5035, -100.67761
5generate(0.34073696, 0.93847651, -0.05621475), (-0.87698289, 0.33882051, 0.34073714), (0.33882034, -0.06680236, 0.93847651)-39.83594, 213.9051, -37.60222
6generate(-0.63291429, -0.24476197, 0.73451426), (-0.2447618, -0.83680003, -0.48975219), (0.73451416, -0.48975247, 0.46971432)204.21165, 459.33321, 51.0053
7generate(-0.4866513, 0.72240082, 0.49123071), (-0.8411853, -0.23574964, -0.48665102), (-0.23574981, -0.65004541, 0.72240093)48.77158, 457.95269, 207.82589
8generate(0.48452163, 0.83892942, 0.24786297), (-0.48051161, 0.49200835, -0.72597275), (-0.73099065, 0.23264864, 0.64150401)-102.05813, 306.26978, 153.06343
9generate(0.93847651, -0.05621475, 0.34073696), (0.33882051, 0.34073714, -0.87698289), (-0.06680236, 0.93847651, 0.33882034)-39.83594, 213.9051, -37.60222
10generate(0.24786314, -0.72597286, 0.641504), (0.48452191, -0.4805116, -0.73099054), (0.83892942, 0.49200807, 0.23264847)149.44919, 308.5035, -100.67761
11generate(-0.83680003, -0.48975219, -0.2447618), (-0.48975247, 0.46971432, 0.73451416), (-0.24476197, 0.73451426, -0.63291429)459.33321, 51.0053, 204.21165
12generate(-0.73099054, 0.48452191, -0.4805116), (0.23264847, 0.83892942, 0.49200807), (0.641504, 0.24786314, -0.72597286)308.5035, -100.67761, 149.44919
13generate(0.23264864, 0.64150401, -0.73099065), (0.83892942, 0.24786297, 0.48452163), (0.49200835, -0.72597275, -0.48051161)153.06343, -102.05813, 306.26978
14generate(0.72240093, -0.23574981, -0.65004541), (0.49123071, -0.4866513, 0.72240082), (-0.48665102, -0.8411853, -0.23574964)207.82589, 48.77158, 457.95269
15generate(0.06144531, -0.93490459, -0.34953945), (-0.32993985, -0.34953962, 0.8769047), (-0.94200013, 0.06144531, -0.32993967)397.11102, 143.36998, 394.8773
16generate(0.46971432, 0.73451416, -0.48975247), (0.73451426, -0.63291429, -0.24476197), (-0.48975219, -0.2447618, -0.83680003)51.0053, 204.21165, 459.33321
17generate(0.8769047, -0.32993985, -0.34953962), (-0.32993967, -0.94200013, 0.06144531), (-0.34953945, 0.06144531, -0.93490459)143.36998, 394.8773, 397.11102
18generate(0.00880248, -0.99992182, -0.00888067), (-0.99992182, -0.00888067, 0.00880248), (-0.00888067, 0.00880248, -0.99992182)357.27508, 357.27508, 357.27508
19generate(-0.93490459, -0.34953945, 0.06144531), (-0.34953962, 0.8769047, -0.32993985), (0.06144531, -0.32993967, -0.94200013)397.11102, 143.36998, 394.8773
20generate(-0.65004541, 0.72240093, -0.23574981), (0.72240082, 0.49123071, -0.4866513), (-0.23574964, -0.48665102, -0.8411853)207.82589, 48.77158, 457.95269

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Components

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


Mass: 30765.572 Da / Num. of mol.: 7 / Mutation: W336F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage HK97 (virus) / Genus: Lambda-like viruses / Gene: 5 / Plasmid: pT7-Hd2.9 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P49861

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 6.8 Å3/Da / Density % sol: 82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes, 0.2M CaCl2, 2-3% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 5.2→30 Å / Num. obs: 373697 / % possible obs: 83.9 % / Observed criterion σ(F): -1.5 / Observed criterion σ(I): -1.5 / Redundancy: 5.4 % / Rmerge(I) obs: 0.178 / Net I/σ(I): 3.7
Reflection shellResolution: 5.2→5.32 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 1.7 / % possible all: 30.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
RAVEmodel building
CNS1.1refinement
RAVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IF0

1if0


Resolution: 5.2→30 Å / σ(F): 0
RfactorNum. reflection
Rwork0.41 -
all0.41 -
obs0.41 354912
Displacement parametersBiso mean: 112 Å2
Refinement stepCycle: LAST / Resolution: 5.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13797 0 0 0 13797
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008744
X-RAY DIFFRACTIONc_angle_deg1.34583

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