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- PDB-6xxz: Crystal structure of a de novo designed parallel four-helix coile... -

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Basic information

Entry
Database: PDB / ID: 6xxz
TitleCrystal structure of a de novo designed parallel four-helix coiled coil, 2-EK-4
Components2-EK-4
KeywordsDE NOVO PROTEIN / coiled coil / tetramer / parallel
Function / homologyPROPANOIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsEdgell, C.L. / Savery, N.J. / Woolfson, D.N.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S002820/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)EP/L016494/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/L016494/1 United Kingdom
CitationJournal: Biochemistry / Year: 2020
Title: RobustDe Novo-Designed Homotetrameric Coiled Coils.
Authors: Edgell, C.L. / Savery, N.J. / Woolfson, D.N.
History
DepositionJan 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-EK-4
B: 2-EK-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0724
Polymers6,9242
Non-polymers1482
Water73941
1
A: 2-EK-4
B: 2-EK-4
hetero molecules

A: 2-EK-4
B: 2-EK-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1448
Polymers13,8484
Non-polymers2964
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445-x-1/2,-y-1/2,z1
Buried area6850 Å2
ΔGint-46 kcal/mol
Surface area7460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.560, 50.840, 43.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

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Components

#1: Protein/peptide 2-EK-4


Mass: 3462.024 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.92 Å3/Da / Density % sol: 35.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M sodium propionate, 0.1 M sodium cacodylate trihydrate, 0.1 M bis-tris propane, 25% PEG1500, pH 7.0, supplemented with 25% glycerol for cryo-protection

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→43.94 Å / Num. obs: 6093 / % possible obs: 99.6 % / Redundancy: 7.9 % / Biso Wilson estimate: 19.73 Å2 / CC1/2: 0.99 / Net I/σ(I): 12.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 308 / CC1/2: 0.978 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16-3546refinement
iMOSFLM7.2.2data reduction
Aimlessdata scaling
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→43.94 Å / SU ML: 0.1526 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.4615
RfactorNum. reflection% reflection
Rfree0.2143 333 5.48 %
Rwork0.1826 --
obs0.1843 6073 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.34 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms488 0 10 41 539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057512
X-RAY DIFFRACTIONf_angle_d0.7346682
X-RAY DIFFRACTIONf_chiral_restr0.040374
X-RAY DIFFRACTIONf_plane_restr0.002990
X-RAY DIFFRACTIONf_dihedral_angle_d9.1899452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-2.140.25781540.20082811X-RAY DIFFRACTION99.03
2.14-43.940.2031790.17682929X-RAY DIFFRACTION99.14
Refinement TLS params.Method: refined / Origin x: -15.0354676102 Å / Origin y: -8.20651094721 Å / Origin z: 13.7493872719 Å
111213212223313233
T0.120189780398 Å20.0205371659337 Å2-0.0131941116543 Å2-0.116027671966 Å2-0.00342935850829 Å2--0.150212899236 Å2
L1.57492447424 °2-0.0555800294893 °20.195168492589 °2-1.3441810717 °20.528880042577 °2--4.44472700109 °2
S-0.0365362949084 Å °0.0955745816976 Å °0.0182162645218 Å °-0.0832051964024 Å °-0.0783525238114 Å °0.0835667362148 Å °-0.352165313136 Å °-0.352609849801 Å °0.126712858797 Å °
Refinement TLS groupSelection details: all

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