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- PDB-1hgv: Filamentous Bacteriophage PH75 -

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Basic information

Entry
Database: PDB / ID: 1hgv
TitleFilamentous Bacteriophage PH75
ComponentsPH75 INOVIRUS MAJOR COAT PROTEIN
KeywordsVIRUS / VIRUS COAT PROTEIN / HELICAL VIRUS COAT PROTEIN / SSDNA VIRUSES / INOVIRUS / FILAMENTOUS BACTERIOPHAGE / THERMOPHILES / MEMBRANE PROTEINS / ICOSAHEDRAL VIRUS
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #80 / Bacteriophage M13, G8P, capsid domain superfamily / helical viral capsid / host cell membrane / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / membrane / Capsid protein G8P
Function and homology information
Biological speciesBACTERIOPHAGE PH75 (virus)
MethodFIBER DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPederson, D.M. / Welsh, L.C. / Marvin, D.A. / Sampson, M. / Perham, R.N. / Yu, M. / Slater, M.R.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: The Protein Capsid of Filamentous Bacteriophage Ph75 from Thermus Thermophilus
Authors: Pederson, D.M. / Welsh, L.C. / Marvin, D.A. / Sampson, M. / Perham, R.N. / Yu, M. / Slater, M.R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: The Molecular Structure and Structural Transition of the Alpha-Helical Capsid in Filamentous Bacteriophage Pf1
Authors: Welsh, L.C. / Symmons, M.F. / Marvin, D.A.
#2: Journal: J.Mol.Biol. / Year: 1998
Title: Structure of the Capsid of Pf3 Filamentous Phage Determined from X-Ray Fibre Diffraction Data at 3.1 A Resolution
Authors: Welsh, L.C. / Symmons, M.F. / Sturtevant, J.M. / Marvin, D.A. / Perham, R.N.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Pf1 Filamentous Bacteriophage: Refinement of a Molecular Model by Simulated Annealing Using 3.3 Angstroms Resolution X-Ray Fibre Diffraction Data
Authors: Gonzalez, A. / Nave, C. / Marvin, D.A.
#4: Journal: Int.J.Biol.Macromol. / Year: 1990
Title: Model-Building Studies of Inovirus: Genetic Variations on a Geometric Theme
Authors: Marvin, D.A.
History
DepositionDec 15, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Remark 285 THE ANALOGUE OF THE CRYSTALLOGRAPHIC SPACE GROUP FOR HELICAL STRUCTURES IS THE LINE GROUP (A.KLUG, ... THE ANALOGUE OF THE CRYSTALLOGRAPHIC SPACE GROUP FOR HELICAL STRUCTURES IS THE LINE GROUP (A.KLUG, F.H.C.CRICK, H.W.WYCKOFF, ACTA CRYSTALLOG. V.11, 199, 1958). THE LINE GROUP OF PF1 IS S. THE UNIT CELL DIMENSIONS ARE THE HELIX PARAMETERS (UNIT TWIST TAU, UNIT HEIGHT P). THE INDEXING OF UNITS ALONG THE BASIC HELIX IS ILLUSTRATED IN REFERENCE 4. TO GENERATE COORDINATES X(K), Y(K), Z(K) OF UNIT K FROM THE GIVEN COORDINATES X(0), Y(0), Z(0) OF UNIT 0 IN A UNIT CELL WITH HELIX PARAMETERS (TAU, P) = (66.667, 2.90), APPLY THE MATRIX AND VECTOR: | COS(TAU*K) -SIN(TAU*K) 0 | | 0 | | SIN(TAU*K) COS(TAU*K) 0 | + | 0 | | 0 0 1 | | P*K | THE NEIGHBORS IN CONTACT WITH UNIT 0 ARE UNITS K = +/-1, +/-5, +/-6, +/-11 AND +/-17. THESE SYMMETRY-RELATED COPIES ARE USED TO DETERMINE INTERCHAIN NON-BONDED CONTACTS DURING THE REFINEMENT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PH75 INOVIRUS MAJOR COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)4,8171
Polymers4,8171
Non-polymers00
Water00
1
A: PH75 INOVIRUS MAJOR COAT PROTEIN
x 35


Theoretical massNumber of molelcules
Total (without water)168,58035
Polymers168,58035
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation34
identity operation1_555x,y,z1
2


  • Idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)1.000, 1.000, 1.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number1
Space group name H-MP1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 35 / Rise per n subunits: 2.9 Å / Rotation per n subunits: 66.667 °)

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Components

#1: Protein/peptide PH75 INOVIRUS MAJOR COAT PROTEIN / PH75 BACTERIOPHAGE MAJOR COAT PROTEIN


Mass: 4816.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MAJOR COAT PROTEIN ASSEMBLY / Source: (gene. exp.) BACTERIOPHAGE PH75 (virus) / Description: GROWN IN THERMUS THERMOPHILUS / Production host: THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: P82889

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Experimental details

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Experiment

ExperimentMethod: FIBER DIFFRACTION

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Sample preparation

CrystalDescription: THE DATA IS DERIVED FROM CONTINUOUS TRANSFORM DATA AND THEREFORE THE NUMBER OF UNIQUE REFLECTIONS IS A MEANINGLESS NUMBER.
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999 / Details: MIRRORS
RadiationMonochromator: GE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / % possible obs: 100 %
Reflection
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
FXPLORrefinement
CCP13(LSQINT)data reduction
CCP13-FDSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IFN

1ifn


Resolution: 2.4→50 Å / σ(F): 0
Details: THE MODEL WAS DERIVED FROM PDB ENTRY 1IFN, REFERENCE 1, BY MOLECULAR REPLACEMENT
Rfactor% reflection
Rfree0.4 10 %
Rwork0.22 -
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms340 0 0 0 340
Refine LS restraints
Refine-IDTypeDev ideal
FIBER DIFFRACTIONo_bond_d0.019
FIBER DIFFRACTIONo_bond_d_na
FIBER DIFFRACTIONo_bond_d_prot
FIBER DIFFRACTIONo_angle_d
FIBER DIFFRACTIONo_angle_d_na
FIBER DIFFRACTIONo_angle_d_prot
FIBER DIFFRACTIONo_angle_deg1.7
FIBER DIFFRACTIONo_angle_deg_na
FIBER DIFFRACTIONo_angle_deg_prot
FIBER DIFFRACTIONo_dihedral_angle_d23
FIBER DIFFRACTIONo_dihedral_angle_d_na
FIBER DIFFRACTIONo_dihedral_angle_d_prot
FIBER DIFFRACTIONo_improper_angle_d
FIBER DIFFRACTIONo_improper_angle_d_na
FIBER DIFFRACTIONo_improper_angle_d_prot
FIBER DIFFRACTIONo_mcbond_it
FIBER DIFFRACTIONo_mcangle_it
FIBER DIFFRACTIONo_scbond_it
FIBER DIFFRACTIONo_scangle_it
Software
*PLUS
Name: FXPLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19 / Rfactor Rfree: 0.4
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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