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- PDB-4h8g: crystal structure of a parallel 6-helix coiled coil CC-Hex-IL- 22 -

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Basic information

Entry
Database: PDB / ID: 4h8g
Titlecrystal structure of a parallel 6-helix coiled coil CC-Hex-IL- 22
ComponentsCC-Hex-IL-22
KeywordsDE NOVO PROTEIN / spiral/offset 6-straded coiled coil / N-terminal acetylation / C-terminal amidation
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.699 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 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CC-Hex-IL-22
B: CC-Hex-IL-22
C: CC-Hex-IL-22
D: CC-Hex-IL-22
E: CC-Hex-IL-22
F: CC-Hex-IL-22
I: CC-Hex-IL-22
J: CC-Hex-IL-22
G: CC-Hex-IL-22
H: CC-Hex-IL-22
K: CC-Hex-IL-22
L: CC-Hex-IL-22


Theoretical massNumber of molelcules
Total (without water)39,86112
Polymers39,86112
Non-polymers00
Water5,639313
1
A: CC-Hex-IL-22
D: CC-Hex-IL-22
F: CC-Hex-IL-22
I: CC-Hex-IL-22
J: CC-Hex-IL-22
H: CC-Hex-IL-22


Theoretical massNumber of molelcules
Total (without water)19,9306
Polymers19,9306
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-97 kcal/mol
Surface area10790 Å2
MethodPISA
2
B: CC-Hex-IL-22
C: CC-Hex-IL-22
E: CC-Hex-IL-22
G: CC-Hex-IL-22
K: CC-Hex-IL-22
L: CC-Hex-IL-22


Theoretical massNumber of molelcules
Total (without water)19,9306
Polymers19,9306
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8120 Å2
ΔGint-98 kcal/mol
Surface area10500 Å2
MethodPISA
3
A: CC-Hex-IL-22
D: CC-Hex-IL-22
F: CC-Hex-IL-22
I: CC-Hex-IL-22
J: CC-Hex-IL-22
H: CC-Hex-IL-22

B: CC-Hex-IL-22
C: CC-Hex-IL-22
E: CC-Hex-IL-22
G: CC-Hex-IL-22
K: CC-Hex-IL-22
L: CC-Hex-IL-22


Theoretical massNumber of molelcules
Total (without water)39,86112
Polymers39,86112
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x+1/2,y+1/2,z1
Buried area18290 Å2
ΔGint-210 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.990, 126.800, 127.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailscrystal structure in agreement with solution-phase biophysics (AUC)

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Components

#1: Protein/peptide
CC-Hex-IL-22


Mass: 3321.732 Da / Num. of mol.: 12 / 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.: 313 / 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 %

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0410.97
SYNCHROTRONDiamond I0421.7
Detector
TypeIDDetector
ADSC QUANTUM 3151CCD
ADSC QUANTUM 3152CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
21.71
ReflectionResolution: 1.699→69.2 Å / Num. all: 46763 / Num. obs: 46623

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 1.699→38.4 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.877 / SU B: 2.394 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27974 2364 5.1 %RANDOM
Rwork0.24707 ---
obs0.24873 44355 99.66 %-
all-44488 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.233 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2---0.9 Å2-0 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.699→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 0 313 2985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192672
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1522.0733547
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5015347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6723072
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67615576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.021772
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.699→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.497 151 -
Rwork0.455 3066 -
obs--100 %

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