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- PDB-1aa0: FIBRITIN DELETION MUTANT E (BACTERIOPHAGE T4) -

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Basic information

Entry
Database: PDB / ID: 1aa0
TitleFIBRITIN DELETION MUTANT E (BACTERIOPHAGE T4)
ComponentsFIBRITIN
KeywordsATTACHMENT PROTEIN / BACTERIOPHAGE T4 / FIBRITIN / STRUCTURAL PROTEIN / BACTERIOPHAGE ASSEMBLY
Function / homology6-Phosphogluconate Dehydrogenase, domain 3 / Fibritin C-terminal / Fibritin C-terminal region / virion component / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / Fibritin
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsTao, Y. / Strelkov, S.V. / Mesyanzhinov, V.V. / Rossmann, M.G.
Citation
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.
#1: 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.
#2: 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
DepositionJan 18, 1997Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIBRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9603
Polymers11,8591
Non-polymers1012
Water1,44180
1
A: FIBRITIN
hetero molecules

A: FIBRITIN
hetero molecules

A: FIBRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8809
Polymers35,5773
Non-polymers3036
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11440 Å2
ΔGint-179 kcal/mol
Surface area17000 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)41.200, 41.200, 358.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-484-

CL

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Components

#1: Protein FIBRITIN / GPWAC E


Mass: 11858.980 Da / Num. of mol.: 1 / Fragment: DELETION MUTANT E, DEL(368-486)
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 / Gene (production host): WAC E / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P10104
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.35 Å3/Da / Density % sol: 35.9 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: PROTEIN WAS CRYSTALLIZED AT 22OC USING 34% PEG400, 0.1M ZN ACETATE IN 0.1M MES BUFFER AT PH6.0 AS WELL SOLUTION BY MIXING EQUAL AMOUNT OF WELL SOLUTION AND PROTEIN SOLUTION AT 29MG/ML IN A ...Details: PROTEIN WAS CRYSTALLIZED AT 22OC USING 34% PEG400, 0.1M ZN ACETATE IN 0.1M MES BUFFER AT PH6.0 AS WELL SOLUTION BY MIXING EQUAL AMOUNT OF WELL SOLUTION AND PROTEIN SOLUTION AT 29MG/ML IN A HANGING DROP, vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
129 mg/mlprotein1drop
210 mMTris-HCl1droppH7.5
334 %PEG4001reservoir
40.1 Mzinc acetate1reservoir
50.1 MMES1reservoirpH6.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 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: 2.2→30 Å / Num. obs: 6009 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 46.3 Å2 / Rsym value: 0.053 / Net I/σ(I): 15
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.437 / % possible all: 56.6
Reflection
*PLUS
Num. obs: 6490 / Num. measured all: 57901 / Rmerge(I) obs: 0.053

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: BULK SOLVENT WAS MODELED AS KSOL 0.43, BSOL=160 THE HEAVY ATOM BINDING SITES ARE: PLATINUM -5.404 11.075 17.936 (ONE SITE) LEAD 16.150 3.180 13.990 (ONE SITE) URANYL 16.356 3.037 13.631 AND ...Details: BULK SOLVENT WAS MODELED AS KSOL 0.43, BSOL=160 THE HEAVY ATOM BINDING SITES ARE: PLATINUM -5.404 11.075 17.936 (ONE SITE) LEAD 16.150 3.180 13.990 (ONE SITE) URANYL 16.356 3.037 13.631 AND 29.640 0.464 8.250 (TWO SITES)
RfactorNum. reflection% reflectionSelection details
Rfree0.259 252 4 %RANDOM
Rwork0.216 ---
obs0.216 5727 88.2 %-
Displacement parametersBiso mean: 47.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.2 Å2-4.8 Å20 Å2
2---7.2 Å20 Å2
3---14.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms834 0 2 80 916
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
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: 2.2→2.34 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 16 1.5 %
Rwork0.331 417 -
obs--41.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Refinement
*PLUS
Rfactor obs: 0.216 / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3
LS refinement shell
*PLUS
Rfactor Rfree: 0.34 / Rfactor Rwork: 0.331

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