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- PDB-4ncu: Foldon domain wild type -

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Basic information

Entry
Database: PDB / ID: 4ncu
TitleFoldon domain wild type
ComponentsFibritin
KeywordsVIRAL PROTEIN / trimeric 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 / MOLECULAR REPLACEMENT / Resolution: 1.11 Å
AuthorsGraewert, M.A. / Reiner, A. / Groll, M. / Kiefhaber, T.
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 5, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibritin


Theoretical massNumber of molelcules
Total (without water)3,0841
Polymers3,0841
Non-polymers00
Water1,24369
1
A: Fibritin

A: Fibritin

A: Fibritin


Theoretical massNumber of molelcules
Total (without water)9,2533
Polymers9,2533
Non-polymers00
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 area3050 Å2
ΔGint-22 kcal/mol
Surface area4490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.839, 27.839, 63.527
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein/peptide Fibritin


Mass: 3084.461 Da / Num. of mol.: 1 / 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
Source: (synth.) Enterobacteria phage T4 (virus) / References: UniProt: D9IEJ2, UniProt: P10104*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 200, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 28, 2011
RadiationMonochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.1→30 Å / Num. all: 11404 / Num. obs: 11279 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.35 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 20.4
Reflection shellResolution: 1.1→1.2 Å / Rmerge(I) obs: 0.132 / Mean I/σ(I) obs: 7.8 / % possible all: 97.8

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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: 1RFO

1rfo


Resolution: 1.11→15 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.69 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.141 525 4.8 %RANDOM
Rwork0.12133 ---
obs0.12229 10461 99.47 %-
all-10986 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.026 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.19 Å2-0 Å2
2---0.19 Å2-0 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.11→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms219 0 0 69 288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02225
X-RAY DIFFRACTIONr_bond_other_d0.0070.02209
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.982306
X-RAY DIFFRACTIONr_angle_other_deg0.6353480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54222.72711
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.1961534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.787152
X-RAY DIFFRACTIONr_chiral_restr0.060.231
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021253
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0253
X-RAY DIFFRACTIONr_rigid_bond_restr5.1453434
X-RAY DIFFRACTIONr_sphericity_free31.534514
X-RAY DIFFRACTIONr_sphericity_bonded6.7875484
LS refinement shellResolution: 1.11→1.139 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.157 40 -
Rwork0.126 756 -
obs--99.25 %
Refinement TLS params.Method: refined / Origin x: -5.9649 Å / Origin y: 1.7438 Å / Origin z: 8.2541 Å
111213212223313233
T0.0045 Å20.0004 Å2-0.0011 Å2-0.0028 Å20.002 Å2--0.0028 Å2
L0.6276 °2-0.0904 °2-0.0135 °2-0.4979 °20.0328 °2--0.0023 °2
S-0.009 Å °-0.001 Å °0.0062 Å °-0.0095 Å °0.0083 Å °0.0289 Å °-0.0004 Å °0.0002 Å °0.0008 Å °

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