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- PDB-2o6n: RH4B: designed right-handed coiled coil tetramer with all biologi... -

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Basic information

Entry
Database: PDB / ID: 2o6n
TitleRH4B: designed right-handed coiled coil tetramer with all biological amino acids
ComponentsRH4B designed peptide
KeywordsDE NOVO PROTEIN / RIGHT-HANDED / TETRAMER
Function / homologyYTTERBIUM (II) ION
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.1 Å
AuthorsSales, M. / Alber, T.
CitationJournal: Protein Sci. / Year: 2007
Title: Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids.
Authors: Sales, M. / Plecs, J.J. / Holton, J.M. / Alber, T.
History
DepositionDec 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The sequence was computationally designed to optimize the stability and specificity of a ...SEQUENCE The sequence was computationally designed to optimize the stability and specificity of a right-handed coiled- coil tetramer

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RH4B designed peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1212
Polymers3,9481
Non-polymers1731
Water2,144119
1
A: RH4B designed peptide
hetero molecules

A: RH4B designed peptide
hetero molecules

A: RH4B designed peptide
hetero molecules

A: RH4B designed peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4838
Polymers15,7904
Non-polymers6924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area6620 Å2
ΔGint-80 kcal/mol
Surface area9300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)38.356, 38.356, 49.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-281-

HOH

21A-302-

HOH

31A-304-

HOH

41A-309-

HOH

DetailsThe biological assembly is the tetramer generated from the monomer in the asymmetric unit by the 4 operations: x,y,z; y-1/2,-x+1/2,z; -x,1-y,z; -y+1/2,x+1/2,z.

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Components

#1: Protein/peptide RH4B designed peptide


Mass: 3947.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical peptide synthesis
#2: Chemical ChemComp-YB2 / YTTERBIUM (II) ION


Mass: 173.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Yb
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 10% PEG 4000, 0.1M ammonium sulfate, 0.15M sodium acetate, 10mM ytterbium(II) chloride, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.000,1.2398,1.3858,1.3864
DetectorDetector: IMAGE PLATE / Date: Feb 28, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.23981
31.38581
41.38641
ReflectionResolution: 1→30.36 Å / Num. all: 20717 / Num. obs: 20631 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 8.7 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.074 / Net I/σ(I): 21.09
Reflection shellResolution: 1→1.05 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.011 / Mean I/σ(I) obs: 1.26 / Rsym value: 0.85 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.1→30.36 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.662 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.026 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.132 791 5.1 %RANDOM
Rwork0.115 ---
obs0.116 14797 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.1→30.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms274 0 1 119 394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022312
X-RAY DIFFRACTIONr_bond_other_d0.0010.02339
X-RAY DIFFRACTIONr_angle_refined_deg1.2982.033419
X-RAY DIFFRACTIONr_angle_other_deg0.7293791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.014540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.36229.16712
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1891577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.246
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02340
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0248
X-RAY DIFFRACTIONr_nbd_refined0.3280.289
X-RAY DIFFRACTIONr_nbd_other0.1750.2346
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2170
X-RAY DIFFRACTIONr_nbtor_other0.0830.2182
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2440.273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0790.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3020.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.244
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1670.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9911.5271
X-RAY DIFFRACTIONr_mcbond_other0.7251.574
X-RAY DIFFRACTIONr_mcangle_it2.0332309
X-RAY DIFFRACTIONr_scbond_it4.6183153
X-RAY DIFFRACTIONr_scangle_it5.684.5110
X-RAY DIFFRACTIONr_rigid_bond_restr1.6753775
X-RAY DIFFRACTIONr_sphericity_free11.4645121
X-RAY DIFFRACTIONr_sphericity_bonded4.1755648
LS refinement shellResolution: 1.1→1.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 63 -
Rwork0.227 1073 -
obs--100 %

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