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- PDB-4ncw: foldon domain wild type C-conjugate -

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Basic information

Entry
Database: PDB / ID: 4ncw
Titlefoldon domain wild type C-conjugate
ComponentsFibritin
KeywordsVIRAL PROTEIN / trimeric scaffold / chemical ligation / folding / trazido-functionalized trimesic acid scaffold
Function / homologyFibritin C-terminal / Fibritin C-terminal region / virion component / N,N',N''-triethylbenzene-1,3,5-tricarboxamide / Fibritin / Fibritin
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsGraewert, M.A. / Berthelmann, A. / Lach, J. / Groll, M. / Eichler, J.
CitationJournal: Org.Biomol.Chem. / Year: 2014
Title: Versatile C(3)-symmetric scaffolds and their use for covalent stabilization of the foldon trimer.
Authors: Berthelmann, A. / Lach, J. / Grawert, M.A. / Groll, M. / Eichler, J.
History
DepositionOct 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Fibritin
C: Fibritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5454
Polymers9,2533
Non-polymers2911
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-14 kcal/mol
Surface area4290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.710, 28.100, 55.990
Angle α, β, γ (deg.)90.00, 106.81, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.500592, -0.865683, 0.001175), (0.865682, -0.500593, -0.001252), (0.001672, 0.00039, 0.999999)3.44592, 34.1778, -0.00462
3given(-0.499893, 0.866087, 0.00061), (-0.866087, -0.499893, -0.00092), (-0.000492, -0.000989, 0.999999)-27.78196, 20.17072, 0.00564

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Components

#1: Protein/peptide Fibritin


Mass: 3084.461 Da / Num. of mol.: 3 / Fragment: C-terminus fragment (UNP residues 458-484) / Source method: obtained synthetically
Details: This sequence occurs naturally in bacteriophage T4 fibritin at its C-terminus and harbors an trimesic acid C-conjugate
Source: (synth.) Enterobacteria phage T4 (virus) / References: UniProt: D9IEJ2, UniProt: P10104*PLUS
#2: Chemical ChemComp-2KN / N,N',N''-triethylbenzene-1,3,5-tricarboxamide


Mass: 291.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA TRIMESIC ACID DERIVATIVE WAS USED TO CROSSLINK THE THREE FOLDON SUBUNITS AT THEIR C-NERMINI. ONLY ...A TRIMESIC ACID DERIVATIVE WAS USED TO CROSSLINK THE THREE FOLDON SUBUNITS AT THEIR C-NERMINI. ONLY PART OF THE TRIMESIC ACID IS DEFINED IN THE ELECTRON DENSITY FOR THIS STRUCTURE. IT IS PRESENT AS AN 2KN GROUP IN THE COORDINATES.

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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: 1.98 Å3/Da / Density % sol: 37.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M Ammoniumsulfate, 30% PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2013
RadiationMonochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. all: 19197 / Num. obs: 17100 / % possible obs: 94.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 9.3
Reflection shellResolution: 1.3→1.4 Å / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 3.6 / % possible all: 92.5

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NCU

4ncu


Resolution: 1.3→15 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.063 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.064 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19299 855 5 %RANDOM
Rwork0.16835 ---
obs0.16984 16244 94.54 %-
all-17099 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.645 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0 Å20.24 Å2
2---0.65 Å2-0 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms590 0 21 143 754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02629
X-RAY DIFFRACTIONr_bond_other_d0.0050.02593
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.999852
X-RAY DIFFRACTIONr_angle_other_deg1.0143.011358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.915570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9222330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.6921595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.194156
X-RAY DIFFRACTIONr_chiral_restr0.0870.286
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021701
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02147
X-RAY DIFFRACTIONr_rigid_bond_restr3.64831222
X-RAY DIFFRACTIONr_sphericity_free28.887544
X-RAY DIFFRACTIONr_sphericity_bonded7.51151306
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 61 -
Rwork0.251 1160 -
obs--92.85 %

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