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- PDB-1avy: FIBRITIN DELETION MUTANT M (BACTERIOPHAGE T4) -

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Basic information

Entry
Database: PDB / ID: 1avy
TitleFIBRITIN DELETION MUTANT M (BACTERIOPHAGE T4)
ComponentsFIBRITIN
KeywordsCOILED COIL / BACTERIOPHAGE T4 / STRUCTURAL PROTEIN / CHAPERONE / BACTERIOPHAGE ASSEMBLY / PROTEIN FOLDING
Function / homology6-Phosphogluconate Dehydrogenase, domain 3 / Fibritin C-terminal / Fibritin C-terminal region / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / virion component / Up-down Bundle / Mainly Alpha / Fibritin
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsStrelkov, S.V. / Tao, Y. / Mesyanzhinov, V.V. / Rossmann, M.G.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of bacteriophage T4 fibritin M: a troublesome packing arrangement.
Authors: Strelkov, S.V. / Tao, Y. / Shneider, M.M. / Mesyanzhinov, V.V. / Rossmann, M.G.
#1: Journal: Structure / Year: 1997
Title: Structure of Bacteriophage T4 Fibritin: A Segmented Coiled Coil and the Role of the C-Terminal Domain
Authors: Tao, Y. / Strelkov, S.V. / Mesyanzhinov, V.V. / Rossmann, M.G.
#2: Journal: Virology / Year: 1996
Title: Preliminary Crystallographic Studies of Bacteriophage T4 Fibritin Confirm a Trimeric Coiled-Coil Structure
Authors: Strelkov, S.V. / Tao, Y. / Rossmann, M.G. / Kurochkina, L.P. / Shneider, M.M. / Mesyanzhinov, V.V.
#3: Journal: J.Mol.Biol. / Year: 1994
Title: Fibritin Encoded by Bacteriophage T4 Gene Wac Has a Parallel Triple-Stranded Alpha-Helical Coiled-Coil Structure
Authors: Efimov, V.P. / Nepluev, I.V. / Sobolev, B.N. / Zurabishvili, T.G. / Schulthess, T. / Lustig, A. / Engel, J. / Haener, M. / Aebi, U. / Venyaminov, S.Yu. / Potekhin, S.A. / Mesyanzhinov, V.V.
History
DepositionSep 22, 1997Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.5Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FIBRITIN
B: FIBRITIN
C: FIBRITIN


Theoretical massNumber of molelcules
Total (without water)23,9453
Polymers23,9453
Non-polymers00
Water4,990277
1
A: FIBRITIN

A: FIBRITIN

A: FIBRITIN


Theoretical massNumber of molelcules
Total (without water)23,9453
Polymers23,9453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
2
B: FIBRITIN

B: FIBRITIN

B: FIBRITIN


Theoretical massNumber of molelcules
Total (without water)23,9453
Polymers23,9453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
3
C: FIBRITIN

C: FIBRITIN

C: FIBRITIN


Theoretical massNumber of molelcules
Total (without water)23,9453
Polymers23,9453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)43.680, 43.680, 90.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-276-

HOH

21B-275-

HOH

31C-277-

HOH

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Components

#1: Protein FIBRITIN / GPWAC M


Mass: 7981.825 Da / Num. of mol.: 3
Fragment: DELETION MUTANT M, RESIDUES 413 - 486 OF THE WILD TYPE
Mutation: R416S, S421K, N425I, N428D, T433R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Cell line: BL21 / Gene: WAC / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P10104
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 45 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROPS WITH 20MG/ML PROTEIN AND 1.75M LI2SO4, 0.1M TRIS-HCL, PH7.5, AS PRECIPITANT, vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
25 mMNa phosphate1drop
30.875 M1dropLi2SO4
40.05 MTris-HCl1drop
51.75 M1reservoirLi2SO4
60.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 1, 1995 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→23 Å / Num. obs: 14861 / % possible obs: 89.8 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 20.9 Å2 / Rsym value: 0.036
Reflection shellResolution: 1.85→1.91 Å / Rsym value: 0.182 / % possible all: 53.6
Reflection
*PLUS
Num. measured all: 39783 / Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 53.6 % / Rmerge(I) obs: 0.182

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AA0

1aa0


Resolution: 1.85→23 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT WAS MODELED USING A STANDARD X-PLOR PROCEDURE, WITH BULK SOLVENT DENSITY 0.432 E/A3.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 740 5 %RANDOM
Rwork0.22 ---
obs0.22 14861 89.8 %-
Displacement parametersBiso mean: 32.81 Å2
Refinement stepCycle: LAST / Resolution: 1.85→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 0 277 1718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 1.85→1.93 Å / Rfactor Rfree: 0.416 / Rfactor Rwork: 0.317 / Total num. of bins used: 10
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
LS refinement shell
*PLUS
Rfactor obs: 0.317

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