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- PDB-1ql2: Inovirus (Filamentous Bacteriophage) Strain PF1 Major Coat Protei... -

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Basic information

Entry
Database: PDB / ID: 1ql2
TitleInovirus (Filamentous Bacteriophage) Strain PF1 Major Coat Protein Assembly
ComponentsPF1 BACTERIOPHAGE COAT PROTEIN B
KeywordsVIRUS / VIRUS COAT PROTEIN / HELICAL VIRUS COAT PROTEIN / SSDNA VIRUSES / INOVIRUS / HELICAL VIRUS
Function / homology
Function and homology information


helical viral capsid / host cell membrane / membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #230 / Inovirus Coat protein B / Capsid protein G8P / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPSEUDOMONAS PHAGE PF1 (virus)
MethodFIBER DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWelsh, L.C. / Symmons, M.F. / Marvin, D.A.
Citation
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.
#1: 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.
#2: Journal: Phase Transitions / Year: 1992
Title: Two Forms of Pf1 Inovirus: X-Ray Diffraction Studies on a Structural Phase Transition and a Calculated Libration Normal Mode of the Asymmetric Unit
Authors: Marvin, D.A. / Nave, C. / Bansal, M. / Hale, R.D. / Salje, E.K.H.
#3: Journal: Int.J.Biol.Macromol. / Year: 1990
Title: Model-Building Studies of Inovirus: Genetic Variations on a Geometric Theme
Authors: Marvin, D.A.
#4: Journal: Int.J.Biol.Macromol. / Year: 1989
Title: Dynamics of Telescoping Inovirus: A Mechanism for Assembly at Membrane Adhesions
Authors: Marvin, D.A.
History
DepositionAug 20, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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). FOR THE PERTURBED MODEL OF PF1, TAU = 200. DEGREES, P = 8.70 ANGSTROMS. 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. [ THE LOWER-TEMPERATURE FORM OF PF1 HAS HELIX PARAMETERS, TAU = 65.915 DEGREES, P = 3.05 ANGSTROMS. ]

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PF1 BACTERIOPHAGE COAT PROTEIN B
B: PF1 BACTERIOPHAGE COAT PROTEIN B
C: PF1 BACTERIOPHAGE COAT PROTEIN B


Theoretical massNumber of molelcules
Total (without water)13,8373
Polymers13,8373
Non-polymers00
Water0
1
A: PF1 BACTERIOPHAGE COAT PROTEIN B
B: PF1 BACTERIOPHAGE COAT PROTEIN B
C: PF1 BACTERIOPHAGE COAT PROTEIN B
x 13


Theoretical massNumber of molelcules
Total (without water)179,88339
Polymers179,88339
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation12
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: 13 / Rise per n subunits: 9.15 Å / Rotation per n subunits: 197.745 °)

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Components

#1: Protein/peptide PF1 BACTERIOPHAGE COAT PROTEIN B / PF1 INOVIRUS


Mass: 4612.393 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: MAJOR COAT PROTEIN ASSEMBLY IN THE HIGHER-TEMPERATURE SYMMETRY
Source: (gene. exp.) PSEUDOMONAS PHAGE PF1 (virus) / Description: GROWN IN PSEUDOMONAS AERUGINOSA / Production host: PSEUDOMONAS AERUGINOSA (bacteria) / References: UniProt: P03621

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Experimental details

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Experiment

ExperimentMethod: FIBER DIFFRACTION

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Sample preparation

Crystal growpH: 8 / Details: pH 8.00
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.1 / Method: microdialysis / Details: Nave, C., (1981) J.Mol.Biol., 149, 675.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 mg/mlvirus11
210 mMTris-HCl12

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: GE(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 816 / % 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 2IFN

2ifn


Resolution: 3.1→50 Å / σ(F): 0
Details: THE MODEL WAS DERIVED FROM PDB ENTRY 2IFN, REFERENCE 1. THIS MODEL WAS REFINED AGAINST NEW FIBER DIFFRACTION DATA. THE TEMPERATURE FACTORS OF ENTRY 4IFM WERE USED WITHOUT FURTHER REFINEMENT.
Num. reflection% reflection
obs2448 100 %
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 0 0 966
Refine LS restraints
Refine-IDTypeDev ideal
FIBER DIFFRACTIONo_bond_d0.01
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_deg1.5
FIBER DIFFRACTIONo_angle_deg_na
FIBER DIFFRACTIONo_angle_deg_prot
FIBER DIFFRACTIONo_dihedral_angle_d17
FIBER DIFFRACTIONo_dihedral_angle_d_na
FIBER DIFFRACTIONo_dihedral_angle_d_prot
FIBER DIFFRACTIONo_improper_angle_d1.4
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
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_deg17
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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