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- PDB-4h8o: Crystal structure of a parallel 6-helix coiled coil CC-Hex-N24 -

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Basic information

Entry
Database: PDB / ID: 4h8o
TitleCrystal structure of a parallel 6-helix coiled coil CC-Hex-N24
ComponentsCC-Hex-N24
KeywordsDE NOVO PROTEIN / CC-Hex / parallel / hexameric coiled coil / N-terminal acetylation / C-terminal amidation
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.598 Å
AuthorsChi, B. / Zaccai, N.R. / Brady, R.L. / Woolfson, D.N.
CitationJournal: To be Published
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CC-Hex-N24
B: CC-Hex-N24
C: CC-Hex-N24
D: CC-Hex-N24
E: CC-Hex-N24
F: CC-Hex-N24


Theoretical massNumber of molelcules
Total (without water)19,2776
Polymers19,2776
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9610 Å2
ΔGint-90 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.880, 111.050, 35.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-123-

HOH

21B-125-

HOH

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Components

#1: Protein/peptide
CC-Hex-N24


Mass: 3212.780 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.: 219 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 3% D-sorbitol, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM trisodium citrate, 20 mM sodium potassium L-tartrate, 20 mM sodium oxamate; 100 mM MES/imidazole pH 6.5; and 10 % PEG 20K, ...Details: 3% D-sorbitol, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM trisodium citrate, 20 mM sodium potassium L-tartrate, 20 mM sodium oxamate; 100 mM MES/imidazole pH 6.5; and 10 % PEG 20K, 20 % PEG MME 550, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.598→50.9 Å / Num. all: 27793 / Num. obs: 27487

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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: 1.598→46.256 Å / SU ML: 0.26 / σ(F): 1.04 / Phase error: 32.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 2501 4.99 %
Rwork0.2147 --
obs0.2164 50075 95.95 %
all-50632 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.059 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.7934 Å20 Å20 Å2
2--1.0109 Å2-0 Å2
3---0.7824 Å2
Refinement stepCycle: LAST / Resolution: 1.598→46.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1362 0 0 219 1581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161363
X-RAY DIFFRACTIONf_angle_d1.4651812
X-RAY DIFFRACTIONf_dihedral_angle_d14.56522
X-RAY DIFFRACTIONf_chiral_restr0.094210
X-RAY DIFFRACTIONf_plane_restr0.005234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.598-1.62870.51821190.44692345X-RAY DIFFRACTION84
1.6287-1.66190.47641070.43342470X-RAY DIFFRACTION91
1.6619-1.69810.43671370.41422611X-RAY DIFFRACTION92
1.6981-1.73760.35851360.37972560X-RAY DIFFRACTION94
1.7376-1.7810.35661380.36432585X-RAY DIFFRACTION94
1.781-1.82920.40191380.33982602X-RAY DIFFRACTION94
1.8292-1.8830.38821320.3292580X-RAY DIFFRACTION93
1.883-1.94380.30811390.30542648X-RAY DIFFRACTION97
1.9438-2.01330.30721310.24282669X-RAY DIFFRACTION96
2.0133-2.09390.27671720.21692681X-RAY DIFFRACTION98
2.0939-2.18920.25571390.21392620X-RAY DIFFRACTION97
2.1892-2.30460.25821320.18352740X-RAY DIFFRACTION98
2.3046-2.4490.19571610.16822732X-RAY DIFFRACTION99
2.449-2.6380.22011280.15722755X-RAY DIFFRACTION100
2.638-2.90350.24991500.18482743X-RAY DIFFRACTION100
2.9035-3.32350.21691520.17452732X-RAY DIFFRACTION100
3.3235-4.18690.16811560.15822764X-RAY DIFFRACTION100
4.1869-46.27540.23261340.20812737X-RAY DIFFRACTION99

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