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- PDB-2ibl: Crystal structure of a helper molecule (HT-mf-thromb) based on mi... -

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Basic information

Entry
Database: PDB / ID: 2ibl
TitleCrystal structure of a helper molecule (HT-mf-thromb) based on mini-fibritin (mf) crystal structure (pdb:1OX3).
ComponentsFibritin
KeywordsCHAPERONE / mini-fibritin / foldon / trimerization / bacteriophage t4 / helper molecule
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 / Fibritin
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
Enterobacteria phage Ox2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsBoudko, S.P. / Rossmann, M.G.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: The Coiled-coil Domain Structure of the Sin Nombre Virus Nucleocapsid Protein.
Authors: Boudko, S.P. / Kuhn, R.J. / Rossmann, M.G.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Structure formation in the C terminus of type III collagen guides disulfide cross-linking
Authors: Boudko, S.P. / Engel, J.
#2: Journal: 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
DepositionSep 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Sep 10, 2014Group: Database references
Revision 1.4Jun 14, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity_name_com / entity_src_gen ...entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_name_com.name / _struct_ref.pdbx_align_begin ..._entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 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)14,0621
Polymers14,0621
Non-polymers00
Water3,549197
1
A: Fibritin

A: Fibritin

A: Fibritin


Theoretical massNumber of molelcules
Total (without water)42,1853
Polymers42,1853
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area10590 Å2
ΔGint-85 kcal/mol
Surface area15900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.677, 53.677, 106.458
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-262-

HOH

21A-263-

HOH

31A-264-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: x,y,z; -x+y+1,-x,z; -y,x-y-1,z

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Components

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


Mass: 14061.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Enterobacteria phage Ox2 (virus)
Gene: wac / Plasmid: pET23d(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P10104, UniProt: Q38650
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 30% PEG 400, 0.1 M TrisHCl, 0.2 M magnesium chloride, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.00465 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 30, 2005
Details: Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00465 Å / Relative weight: 1
ReflectionResolution: 1.32→35 Å / Num. all: 40437 / Num. obs: 40028 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 31.7
Reflection shellResolution: 1.32→1.354 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 5.2 / Num. unique all: 2823 / Rsym value: 0.216 / % possible all: 89.71

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OX3

1ox3


Resolution: 1.32→35 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.972 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.041 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17 2001 5 %RANDOM
Rwork0.16 ---
all0.161 39993 --
obs0.161 39993 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.117 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.32→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms833 0 0 197 1030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022867
X-RAY DIFFRACTIONr_bond_other_d0.0010.02589
X-RAY DIFFRACTIONr_angle_refined_deg1.0121.9761178
X-RAY DIFFRACTIONr_angle_other_deg0.82531452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8165107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.65625.36641
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.49915155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.487156
X-RAY DIFFRACTIONr_chiral_restr0.0580.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02955
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02157
X-RAY DIFFRACTIONr_nbd_refined0.210.2150
X-RAY DIFFRACTIONr_nbd_other0.180.2608
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2429
X-RAY DIFFRACTIONr_nbtor_other0.0790.2456
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2106
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.233
X-RAY DIFFRACTIONr_mcbond_it1.1211.5705
X-RAY DIFFRACTIONr_mcbond_other0.5441.5219
X-RAY DIFFRACTIONr_mcangle_it1.3492879
X-RAY DIFFRACTIONr_scbond_it2.1263376
X-RAY DIFFRACTIONr_scangle_it2.8344.5299
LS refinement shellResolution: 1.32→1.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 129 -
Rwork0.174 2591 -
obs-2720 89.71 %

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