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- PDB-4ncv: Foldon domain wild type N-conjugate -

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Basic information

Entry
Database: PDB / ID: 4ncv
TitleFoldon domain wild type N-conjugate
ComponentsFibritin
KeywordsVIRAL PROTEIN / trimeric scaffold / chemical ligation / folding / trazido-functionalized trimesic acid scaffold
Function / homologyFibritin C-terminal / Fibritin C-terminal region / virion component / Fibritin / Fibritin
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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


Theoretical massNumber of molelcules
Total (without water)9,3313
Polymers9,3313
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-23 kcal/mol
Surface area4680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.970, 47.930, 27.970
Angle α, β, γ (deg.)90.00, 92.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Fibritin


Mass: 3110.499 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 N-conjugate
Source: (synth.) Enterobacteria phage T4 (virus) / References: UniProt: D9IEJ2, UniProt: P10104*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA TRIMESIC ACID DERIVATIVE WAS USED TO CROSSLINK THE THREE FOLDON SUBUNITS AT THEIR N-NERMINI. ONLY ...A TRIMESIC ACID DERIVATIVE WAS USED TO CROSSLINK THE THREE FOLDON SUBUNITS AT THEIR N-NERMINI. ONLY PART OF THE TRIMESIC ACID IS DEFINED IN THE ELECTRON DENSITY FOR THIS STRUCTURE. IT IS PRESENT AS AN ACE 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: 2.01 Å3/Da / Density % sol: 38.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.4 M Na/K-phosphate, pH 5, 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: Jul 6, 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: 1.2→30 Å / Num. obs: 22182 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 15.7
Reflection shellResolution: 1.2→1.3 Å / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.3 / % possible all: 91.9

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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: 1.2→15 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.332 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.039 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16317 1109 5 %RANDOM
Rwork0.13346 ---
obs0.1349 21062 95.86 %-
all-22171 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.351 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å2-0.05 Å2
2--0.15 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms663 0 0 126 789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02681
X-RAY DIFFRACTIONr_bond_other_d0.0010.02625
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.98926
X-RAY DIFFRACTIONr_angle_other_deg0.71631434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.897580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.0322.72733
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.6415102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.526156
X-RAY DIFFRACTIONr_chiral_restr0.070.293
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021773
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02161
X-RAY DIFFRACTIONr_rigid_bond_restr1.53531302
X-RAY DIFFRACTIONr_sphericity_free22.615532
X-RAY DIFFRACTIONr_sphericity_bonded5.80251378
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 77 -
Rwork0.258 1458 -
obs--89.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1993-0.26420.11490.3863-0.09080.1742-0.0195-0.0222-0.02170.01080.02930.0318-0.0318-0.0152-0.00990.0123-0.0004-0.00260.010.00030.00760.9557-2.394530.8845
20.2786-0.0137-0.01670.50480.07870.1701-0.0308-0.04010.01690.01720.0509-0.0646-0.03550.0299-0.02020.0140.0009-0.00160.0138-0.00780.014911.4084-2.737832.9509
30.1998-0.1547-0.02820.77640.21590.1022-0.03780.0248-0.031-0.03350.0542-0.00380.01860.0361-0.01630.03760.0017-0.00140.0204-0.00980.01326.766-10.042826.4926
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 27
2X-RAY DIFFRACTION2B0 - 27
3X-RAY DIFFRACTION3C1 - 27

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