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- PDB-6q5q: Crystal structure of a CC-Hex mutant that forms an antiparallel f... -

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Basic information

Entry
Database: PDB / ID: 6q5q
TitleCrystal structure of a CC-Hex mutant that forms an antiparallel four-helix coiled coil CC-Hex-KgEb
ComponentsCC-Hex-KgEb
KeywordsDE NOVO PROTEIN / coiled coil / tetramer / synthetic / antiparallel
Function / homologyL(+)-TARTARIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.08 Å
AuthorsZaccai, N.R. / Rhys, G.G. / Wood, C.W. / Beesley, J.L. / Brady, R.L. / Woolfson, D.N.
Funding support United Kingdom, Belgium, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J014400/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/G036764/1 United Kingdom
European Research Council340764 Belgium
Biotechnology and Biological Sciences Research CouncilBB/R00661X/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/K03927X/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Navigating the Structural Landscape of De Novo alpha-Helical Bundles.
Authors: Rhys, G.G. / Wood, C.W. / Beesley, J.L. / Zaccai, N.R. / Burton, A.J. / Brady, R.L. / Thomson, A.R. / Woolfson, D.N.
History
DepositionDec 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CC-Hex-KgEb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5132
Polymers3,3631
Non-polymers1501
Water61334
1
A: CC-Hex-KgEb
hetero molecules

A: CC-Hex-KgEb
hetero molecules

A: CC-Hex-KgEb
hetero molecules

A: CC-Hex-KgEb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0528
Polymers13,4524
Non-polymers6004
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area6500 Å2
ΔGint-64 kcal/mol
Surface area8490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.570, 29.350, 55.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-231-

HOH

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Components

#1: Protein/peptide CC-Hex-KgEb


Mass: 3363.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Antiparallel four-helix coiled coil / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.74 Å3/Da / Density % sol: 29.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M potassium/sodium tartrate tetrahydrate 20% w/v PEG 3350.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.08→20.47 Å / Num. obs: 10348 / % possible obs: 99.7 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.021 / Rrim(I) all: 0.077 / Net I/σ(I): 17.5
Reflection shellResolution: 1.08→1.14 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 56.2 / Num. unique obs: 1461 / CC1/2: 0.943 / Rrim(I) all: 0.737 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
SCALAdata scaling
ACORNphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.08→16.5 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.1 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.028 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14659 497 4.8 %RANDOM
Rwork0.13472 ---
obs0.13531 9818 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.091 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å20 Å2
2---0.56 Å20 Å2
3----0.75 Å2
Refinement stepCycle: 1 / Resolution: 1.08→16.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms238 0 10 34 282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.013255
X-RAY DIFFRACTIONr_bond_other_d0.0010.017263
X-RAY DIFFRACTIONr_angle_refined_deg2.2221.682342
X-RAY DIFFRACTIONr_angle_other_deg1.781.596613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.025533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.40126.1119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.6711551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.160.236
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02285
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0239
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_it0.7391.061131
X-RAY DIFFRACTIONr_mcbond_other0.6781.044129
X-RAY DIFFRACTIONr_mcangle_it0.9871.579162
X-RAY DIFFRACTIONr_mcangle_other0.9511.578162
X-RAY DIFFRACTIONr_scbond_it2.8951.636124
X-RAY DIFFRACTIONr_scbond_other2.8631.612121
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5832.21178
X-RAY DIFFRACTIONr_long_range_B_refined3.41815.391299
X-RAY DIFFRACTIONr_long_range_B_other2.8814.429288
X-RAY DIFFRACTIONr_rigid_bond_restr4.1843518
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.082→1.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 40 -
Rwork0.311 710 -
obs-997 99.86 %

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