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- PDB-6q5m: Crystal structure of a CC-Hex mutant that forms an antiparallel f... -

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Basic information

Entry
Database: PDB / ID: 6q5m
TitleCrystal structure of a CC-Hex mutant that forms an antiparallel four-helix coiled coil CC-Hex*-L24Dab
ComponentsCC-Hex*-L24Dab
KeywordsDE NOVO PROTEIN / coiled coil / tetramer / synthetic / antiparallel / CC-Hex
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWood, C.W. / Beesley, J.L. / Rhys, G.G. / 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
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CC-Hex*-L24Dab
B: CC-Hex*-L24Dab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4673
Polymers6,4442
Non-polymers231
Water70339
1
A: CC-Hex*-L24Dab
B: CC-Hex*-L24Dab
hetero molecules

A: CC-Hex*-L24Dab
B: CC-Hex*-L24Dab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9336
Polymers12,8874
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area4740 Å2
ΔGint-60 kcal/mol
Surface area6390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.380, 71.380, 35.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-102-

HOH

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Components

#1: Protein/peptide CC-Hex*-L24Dab


Mass: 3221.832 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.11 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.8 M Na/K hydrogen phosphate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9783 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9783 Å / Relative weight: 1
ReflectionResolution: 1.5→35.72 Å / Num. obs: 8775 / % possible obs: 98.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 16.469 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.036 / Rrim(I) all: 0.061 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.5-1.534.41.1731.14330.7030.6191.331100
8.22-35.693.90.01543.16610.0090.01889.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
Aimless0.7.1data scaling
PHASER7.0.06phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→35.72 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.944 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.081 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22386 447 5.1 %RANDOM
Rwork0.19233 ---
obs0.19413 8322 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.245 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20.33 Å20 Å2
2--0.66 Å20 Å2
3----2.14 Å2
Refinement stepCycle: 1 / Resolution: 1.5→35.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms380 0 1 39 420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013422
X-RAY DIFFRACTIONr_bond_other_d0.0010.017441
X-RAY DIFFRACTIONr_angle_refined_deg1.821.641566
X-RAY DIFFRACTIONr_angle_other_deg1.5241.5931028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.303556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.36825.62516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6041590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.256
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02474
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0270
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_it3.0252.812222
X-RAY DIFFRACTIONr_mcbond_other2.9672.81222
X-RAY DIFFRACTIONr_mcangle_it4.3264.141280
X-RAY DIFFRACTIONr_mcangle_other4.3194.163281
X-RAY DIFFRACTIONr_scbond_it4.463.188199
X-RAY DIFFRACTIONr_scbond_other4.3753.151197
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9044.541286
X-RAY DIFFRACTIONr_long_range_B_refined8.00333.133510
X-RAY DIFFRACTIONr_long_range_B_other7.82632.456501
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 18 -
Rwork0.31 622 -
obs--99.53 %

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