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- PDB-2ww7: foldon containing beta-turn mimic -

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Basic information

Entry
Database: PDB / ID: 2ww7
Titlefoldon containing beta-turn mimic
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: 1.06 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_alt_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FIBRITIN
B: FIBRITIN
C: FIBRITIN
D: FIBRITIN
E: FIBRITIN
F: FIBRITIN


Theoretical massNumber of molelcules
Total (without water)18,8206
Polymers18,8206
Non-polymers00
Water8,053447
1
A: FIBRITIN
B: FIBRITIN
C: FIBRITIN


Theoretical massNumber of molelcules
Total (without water)9,4103
Polymers9,4103
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-10.2 kcal/mol
Surface area4230 Å2
MethodPISA
2
D: FIBRITIN
E: FIBRITIN
F: FIBRITIN


Theoretical massNumber of molelcules
Total (without water)9,4103
Polymers9,4103
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-7.9 kcal/mol
Surface area4280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.730, 28.500, 48.755
Angle α, β, γ (deg.)77.25, 88.00, 69.45
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
FIBRITIN / T4 FIBRITIN


Mass: 3136.620 Da / Num. of mol.: 6 / Fragment: FOLDON, RESIDUES 459-484 / Source method: obtained synthetically / Source: (synth.) ENTEROBACTERIA PHAGE T4 (virus) / References: UniProt: Q76VI8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsGAMMA-5R-HYDROXY-THERONINE (TH6): GAMMA-5R-HYDROXY-THERONINE WAS DIRECTLY LINKED TO PRS VIA CG ...GAMMA-5R-HYDROXY-THERONINE (TH6): GAMMA-5R-HYDROXY-THERONINE WAS DIRECTLY LINKED TO PRS VIA CG FORMING PLICAT L-THIOPROLINE (PRS): L-THIOPROLINE WAS DIRECTLY LINKED TO TH6 VIA CD FORMING PLICAT
Sequence detailsG1 WAS DELETED, Y2 WAS REPLACED BY NA8, FOR G10 A D-AMINO ACID WAS INTRODUCED (DAL), D17 AND G18 ...G1 WAS DELETED, Y2 WAS REPLACED BY NA8, FOR G10 A D-AMINO ACID WAS INTRODUCED (DAL), D17 AND G18 WERE REPLACED BY B-TURN MIMIC

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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 Å3/Da / Density % sol: 36.63 % / Description: ONLY THE FOLDON PART OF THE STRUCTURE WAS USED
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: 1.06→40 Å / Num. obs: 58056 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 4.41 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 19.2
Reflection shellResolution: 1.06→1.12 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 9.5 / % possible all: 86.8

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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: 1.06→26.02 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.711 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES HAVE BEEN REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.14024 1170 2 %RANDOM
Rwork0.10766 ---
obs0.10832 56886 94.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.441 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20.29 Å20.28 Å2
2--0.18 Å20.06 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.06→26.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1332 0 0 447 1779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221669
X-RAY DIFFRACTIONr_bond_other_d0.0030.021592
X-RAY DIFFRACTIONr_angle_refined_deg2.8092.0772323
X-RAY DIFFRACTIONr_angle_other_deg2.52533578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8395202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.7421.89979
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42515291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3011518
X-RAY DIFFRACTIONr_chiral_restr0.1530.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211837
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02403
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_it2.843932
X-RAY DIFFRACTIONr_mcbond_other1.0863352
X-RAY DIFFRACTIONr_mcangle_it3.68341563
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9353737
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1094739
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.96833261
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.061→1.089 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.159 65 -
Rwork0.113 3629 -
obs--81.85 %

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