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- PDB-4h8m: Crystal structure of a parallel 6-helix coiled coil CC-Hex-H24-A5/7C -

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Basic information

Entry
Database: PDB / ID: 4h8m
TitleCrystal structure of a parallel 6-helix coiled coil CC-Hex-H24-A5/7C
ComponentsCC-Hex-H24-A5/7C
KeywordsDE NOVO PROTEIN / CC-Hex / 6-stranded coiled coil / parallel / disulfide bonds / N-terminal acetylation / C-terminal amidation
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4292 Å
AuthorsChi, B. / Zaccai, N.R. / Brady, R.L. / Woolfson, D.N.
CitationJournal: To be Published
Title: TBD
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 1.2Nov 20, 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-H24-A5/7C
B: CC-Hex-H24-A5/7C


Theoretical massNumber of molelcules
Total (without water)6,6482
Polymers6,6482
Non-polymers00
Water1,00956
1
A: CC-Hex-H24-A5/7C
B: CC-Hex-H24-A5/7C

A: CC-Hex-H24-A5/7C
B: CC-Hex-H24-A5/7C

A: CC-Hex-H24-A5/7C
B: CC-Hex-H24-A5/7C


Theoretical massNumber of molelcules
Total (without water)19,9446
Polymers19,9446
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8310 Å2
ΔGint-90 kcal/mol
Surface area9450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.700, 31.700, 132.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-119-

HOH

21A-120-

HOH

31A-121-

HOH

41A-122-

HOH

51A-123-

HOH

61A-124-

HOH

71A-127-

HOH

81B-119-

HOH

91B-120-

HOH

DetailsDisulfide-bridged parallel hexameric coiled coil in redox conditions

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Components

#1: Protein/peptide CC-Hex-H24-A5/7C


Mass: 3323.990 Da / Num. of mol.: 2 / 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.: 56 / 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

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30 mM sodium fluoride, 30 mM sodium bromide, 30 mM sodium iodide, 50 mM sodium HEPES, 50 mM MOPS (acid) pH 7.5, 20 % PEG-MME 550 and 10 % PEG 20K, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.429→44.013 Å / Num. all: 9188 / Num. obs: 9078

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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: 1.4292→44.013 Å / SU ML: 0.17 / σ(F): 0.01 / Phase error: 20.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2035 421 4.78 %
Rwork0.197 --
obs0.1973 8799 95.79 %
all-8906 -
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.999 Å2 / ksol: 0.374 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1091 Å2-0 Å2-0 Å2
2--0.1091 Å20 Å2
3----0.2181 Å2
Refinement stepCycle: LAST / Resolution: 1.4292→44.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms446 0 0 56 502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002473
X-RAY DIFFRACTIONf_angle_d0.573632
X-RAY DIFFRACTIONf_dihedral_angle_d11.683178
X-RAY DIFFRACTIONf_chiral_restr0.04871
X-RAY DIFFRACTIONf_plane_restr0.00276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4292-1.63610.21451550.21432620X-RAY DIFFRACTION90
1.6361-2.06130.2311220.19192836X-RAY DIFFRACTION97
2.0613-44.03420.19351440.19582922X-RAY DIFFRACTION99

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