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- PDB-4h8l: Crystal structure of a parallel 6-helix coiled coil CC-Hex-D24-A5/7C -

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Basic information

Entry
Database: PDB / ID: 4h8l
TitleCrystal structure of a parallel 6-helix coiled coil CC-Hex-D24-A5/7C
ComponentsCC-Hex-D24-A5/7C
KeywordsDE NOVO PROTEIN / CC-Hex / hexameric coiled coil / parallel / N-terminal acetylation / C-terminal amidation
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7501 Å
AuthorsChi, B. / Zaccai, N.R. / Brady, R.L. / Woolfson, D.N.
CitationJournal: J.Am.Chem.Soc.
Title: TBA
Authors: Chi, B. / Zaccai, N.R. / Brady, R.L. / Woolfson, D.N.
History
DepositionSep 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CC-Hex-D24-A5/7C
B: CC-Hex-D24-A5/7C
C: CC-Hex-D24-A5/7C
D: CC-Hex-D24-A5/7C
E: CC-Hex-D24-A5/7C
F: CC-Hex-D24-A5/7C


Theoretical massNumber of molelcules
Total (without water)20,5746
Polymers20,5746
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-86 kcal/mol
Surface area8560 Å2
MethodPISA
2
A: CC-Hex-D24-A5/7C
B: CC-Hex-D24-A5/7C
C: CC-Hex-D24-A5/7C
D: CC-Hex-D24-A5/7C
E: CC-Hex-D24-A5/7C
F: CC-Hex-D24-A5/7C

A: CC-Hex-D24-A5/7C
B: CC-Hex-D24-A5/7C
C: CC-Hex-D24-A5/7C
D: CC-Hex-D24-A5/7C
E: CC-Hex-D24-A5/7C
F: CC-Hex-D24-A5/7C


Theoretical massNumber of molelcules
Total (without water)41,14912
Polymers41,14912
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area19220 Å2
ΔGint-189 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.540, 54.330, 98.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11F-110-

HOH

DetailsSelf-assembling. Disulfides form under redox conditions, Cys 5 - Cys 7' inter-chain linkage

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Components

#1: Protein/peptide
CC-Hex-D24-A5/7C


Mass: 3429.061 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: standard F-moc solid phase peptide synthesis / Source: (synth.) Synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.05 Å3/Da / Density % sol: 39.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30 mM sodium nitrate, 30 mM disodium hydrogen phosphate, 30 mM ammonium sulfate, 100 mM bicine/Trizma base pH 8.5, 12.5 % PEG 1K, 12.5 % PEG 3350, 12.5 % MPD, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.75→36.4 Å / Num. all: 17439 / Num. obs: 16619

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7_650) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R46

3r46


Resolution: 1.7501→30.031 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 25.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2544 816 5 %
Rwork0.2004 --
obs0.203 16306 91.97 %
all-17110 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.423 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4062 Å2-0 Å2-0 Å2
2---3.0157 Å20 Å2
3---3.4219 Å2
Refinement stepCycle: LAST / Resolution: 1.7501→30.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 0 0 110 1306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151222
X-RAY DIFFRACTIONf_angle_d1.3851618
X-RAY DIFFRACTIONf_dihedral_angle_d16.997472
X-RAY DIFFRACTIONf_chiral_restr0.101184
X-RAY DIFFRACTIONf_plane_restr0.005198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.85970.31211030.2731832X-RAY DIFFRACTION67
1.8597-2.00330.26731350.22572431X-RAY DIFFRACTION89
2.0033-2.20480.27841470.18242690X-RAY DIFFRACTION98
2.2048-2.52370.23451480.18122761X-RAY DIFFRACTION99
2.5237-3.17910.25561400.17662825X-RAY DIFFRACTION100
3.1791-30.03580.24531430.21432951X-RAY DIFFRACTION99

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