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- PDB-6v4y: Coiled-coil Trimer with Glu:Tyr:Lys Triad with a K7A mutation -

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Basic information

Entry
Database: PDB / ID: 6v4y
TitleCoiled-coil Trimer with Glu:Tyr:Lys Triad with a K7A mutation
ComponentsCoiled-coil Trimer with Glu:Tyr:Lys Triad with a K7A mutation
KeywordsDE NOVO PROTEIN / Trimer / Helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSmith, M.S. / Stern, K.L. / Billings, W.M. / Price, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorR15 GM116055-01 United States
CitationJournal: Biochemistry / Year: 2020
Title: Context-Dependent Stabilizing Interactions among Solvent-Exposed Residues along the Surface of a Trimeric Helix Bundle.
Authors: Stern, K.L. / Smith, M.S. / Billings, W.M. / Loftus, T.J. / Conover, B.M. / Della Corte, D. / Price, J.L.
History
DepositionDec 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coiled-coil Trimer with Glu:Tyr:Lys Triad with a K7A mutation
B: Coiled-coil Trimer with Glu:Tyr:Lys Triad with a K7A mutation


Theoretical massNumber of molelcules
Total (without water)7,0582
Polymers7,0582
Non-polymers00
Water30617
1
A: Coiled-coil Trimer with Glu:Tyr:Lys Triad with a K7A mutation

A: Coiled-coil Trimer with Glu:Tyr:Lys Triad with a K7A mutation

A: Coiled-coil Trimer with Glu:Tyr:Lys Triad with a K7A mutation


Theoretical massNumber of molelcules
Total (without water)10,5873
Polymers10,5873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area3770 Å2
ΔGint-26 kcal/mol
Surface area5970 Å2
MethodPISA
2
B: Coiled-coil Trimer with Glu:Tyr:Lys Triad with a K7A mutation

B: Coiled-coil Trimer with Glu:Tyr:Lys Triad with a K7A mutation

B: Coiled-coil Trimer with Glu:Tyr:Lys Triad with a K7A mutation


Theoretical massNumber of molelcules
Total (without water)10,5873
Polymers10,5873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3790 Å2
ΔGint-31 kcal/mol
Surface area6020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.814, 39.814, 98.199
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein/peptide Coiled-coil Trimer with Glu:Tyr:Lys Triad with a K7A mutation


Mass: 3529.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 35% 2-ethoxyethanol, 100 mM imidazole/HCl, pH 8, 50 mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5406 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jul 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.85→19.907 Å / Num. obs: 9078 / % possible obs: 99.8 % / Redundancy: 9.4 % / CC1/2: 0.913 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.052 / Rrim(I) all: 0.206 / Net I/σ(I): 17.5
Reflection shellResolution: 1.8501→1.9476 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 990 / CC1/2: 0.822 / Rpim(I) all: 0.261 / Rrim(I) all: 0.523

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6OVS

6ovs


Resolution: 1.85→19.907 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 28.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2468 938 10.33 %
Rwork0.2178 8140 -
obs0.221 9078 91.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.8 Å2 / Biso mean: 23.305 Å2 / Biso min: 10.73 Å2
Refinement stepCycle: final / Resolution: 1.85→19.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms498 0 0 17 515
Biso mean---26.5 -
Num. residues----62
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006504
X-RAY DIFFRACTIONf_angle_d0.732674
X-RAY DIFFRACTIONf_chiral_restr0.02774
X-RAY DIFFRACTIONf_plane_restr0.00384
X-RAY DIFFRACTIONf_dihedral_angle_d2.148310
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8501-1.94760.29291100.257799078
1.9476-2.06950.3131150.2342104882
2.0695-2.22910.2411420.1999110686
2.2291-2.45310.28581270.2262120996
2.4531-2.80720.24511340.23281277100
2.8072-3.53350.29771600.21761244100
3.5335-19.9070.18941500.2044126699

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