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- PDB-1ox3: crystal structure of mini-fibritin -

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Basic information

Entry
Database: PDB / ID: 1ox3
Titlecrystal structure of mini-fibritin
ComponentsFibritin
KeywordsCHAPERONE / foldon / capping motif
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBoudko, S.P. / Stetefeld, J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Design and Crystal Structure of Bacteriophage T4 Mini-Fibritin NCCF.
Authors: Boudko, S.P. / Strelkov, S.V. / Engel, J. / Stetefeld, J.
History
DepositionApr 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jun 28, 2017Group: Advisory / Database references ...Advisory / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_distant_solvent_atoms / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_fragment / _entity_name_com.name ..._entity.pdbx_fragment / _entity_name_com.name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.5Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibritin


Theoretical massNumber of molelcules
Total (without water)11,9141
Polymers11,9141
Non-polymers00
Water1,33374
1
A: Fibritin

A: Fibritin

A: Fibritin


Theoretical massNumber of molelcules
Total (without water)35,7433
Polymers35,7433
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
Buried area10560 Å2
ΔGint-81 kcal/mol
Surface area16140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)54.615, 54.615, 107.848
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-183-

HOH

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Components

#1: Protein Fibritin / Collar protein / Whisker antigen control protein


Mass: 11914.265 Da / Num. of mol.: 1 / Fragment: UNP residues 2-81 and 456-484
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 / Gene: wac / Plasmid: pNCCF / 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.: 74 / 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: 3.66 Å3/Da / Density % sol: 66.1 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 6000, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 277.189 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→24.4 Å / Num. all: 12329 / Num. obs: 12329 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 19.6 Å2 / Rsym value: 0.084 / Net I/σ(I): 5.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1aa0.pdb

1aa0


Resolution: 2→24.36 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 1797080.95 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1268 10.3 %RANDOM
Rwork0.209 ---
all0.216 12329 --
obs0.209 12329 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.6807 Å2 / ksol: 0.315274 e/Å3
Displacement parametersBiso mean: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å21.83 Å20 Å2
2--1.86 Å20 Å2
3----3.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 2→24.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms833 0 0 74 907
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_scangle_it3.422.5
LS refinement shellResolution: 2→2.11 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.242 182 10.3 %
Rwork0.223 1581 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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