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- PDB-2ww6: foldon containing D-amino acids in turn positions -

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Basic information

Entry
Database: PDB / ID: 2ww6
Titlefoldon containing D-amino acids in turn positions
ComponentsFIBRITIN
KeywordsCHAPERONE / D-AMINO ACIDS / VIRAL PROTEIN
Function / homologyFibritin C-terminal / Fibritin C-terminal region / Fibritin
Function and homology information
Biological speciesENTEROBACTERIA PHAGE T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsEckhardt, B. / Grosse, W. / Essen, L.-O. / Geyer, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural Characterization of a Beta-Turn Mimic within a Protein-Protein Interface.
Authors: Eckhardt, B. / Grosse, W. / Essen, L. / Geyer, A.
History
DepositionOct 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. ... SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)9,5864
Polymers9,3923
Non-polymers1941
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-29.5 kcal/mol
Surface area4800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.830, 29.830, 75.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein/peptide FIBRITIN / T4 FIBRITIN


Mass: 3130.573 Da / Num. of mol.: 3 / Fragment: FOLDON, RESIDUES 458-484 / Source method: obtained synthetically / Source: (synth.) ENTEROBACTERIA PHAGE T4 (virus) / References: UniProt: Q76VI8
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Sequence detailsTWO D-AMINO ACIDS WERE INTRODUCED. FOR G10 A D-ALA WAS INTRODUCED, FOR D17 A D-PHE WAS INTRODUCED.

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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: 2.21 Å3/Da / Density % sol: 41.92 %
Description: ONLY FOLDON PART OF STRUCTURE WAS USED AS A MODEL
Crystal growpH: 7 / Details: 9 MM POTASSIUM PHOSPHATE, PH 7.0, 10% D2O

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.7699
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7699 Å / Relative weight: 1
ReflectionResolution: 0.98→20 Å / Num. obs: 42623 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 7.139 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.4
Reflection shellResolution: 0.98→1.03 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.8 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NAY

1nay


Resolution: 0.98→17.98 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.609 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES HAVE BEEN REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.1471 1300 3.1 %RANDOM
Rwork0.12922 ---
obs0.12979 41289 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: SIMPLE SCALING
Displacement parametersBiso mean: 7.614 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å20 Å2
2--0.42 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 0.98→17.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms669 0 11 179 859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022770
X-RAY DIFFRACTIONr_bond_other_d0.0010.02541
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9741064
X-RAY DIFFRACTIONr_angle_other_deg0.8231312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.682596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66921.87532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.6415113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.854156
X-RAY DIFFRACTIONr_chiral_restr0.1010.2112
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021851
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02183
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4172436
X-RAY DIFFRACTIONr_mcbond_other0.3312169
X-RAY DIFFRACTIONr_mcangle_it2.1133717
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6762334
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5413337
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr0.70231311
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.98→1.005 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 65 -
Rwork0.203 3042 -
obs--98.17 %

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