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- PDB-4kvt: Crystal structure of a 6-helix coiled coil CC-Hex-L24C -

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Basic information

Entry
Database: PDB / ID: 4kvt
TitleCrystal structure of a 6-helix coiled coil CC-Hex-L24C
Components6-helix coiled coil CC-Hex-L24C peptide
KeywordsDE NOVO PROTEIN / De Novo Coiled-coil assembly
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBurton, A.J. / Agnew, C. / Brady, R.L. / Woolfson, D.N.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Accessibility, Reactivity, and Selectivity of Side Chains within a Channel of de Novo Peptide Assembly.
Authors: Burton, A.J. / Thomas, F. / Agnew, C. / Hudson, K.L. / Halford, S.E. / Brady, R.L. / Woolfson, D.N.
History
DepositionMay 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-helix coiled coil CC-Hex-L24C peptide
B: 6-helix coiled coil CC-Hex-L24C peptide
C: 6-helix coiled coil CC-Hex-L24C peptide
D: 6-helix coiled coil CC-Hex-L24C peptide
E: 6-helix coiled coil CC-Hex-L24C peptide
F: 6-helix coiled coil CC-Hex-L24C peptide


Theoretical massNumber of molelcules
Total (without water)20,1306
Polymers20,1306
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-106 kcal/mol
Surface area10210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.430, 54.430, 147.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-111-

HOH

21C-101-

HOH

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Components

#1: Protein/peptide
6-helix coiled coil CC-Hex-L24C peptide


Mass: 3354.978 Da / Num. of mol.: 6 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris, 0.1 M potassium chloride with 15 % w/v PEG 2000 MME, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 65 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2012
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.6→34.16 Å / Num. obs: 29509 / % possible obs: 100 % / Observed criterion σ(F): 3.7 / Observed criterion σ(I): 3.7

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→34.098 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2084 1496 5.07 %
Rwork0.1914 --
obs0.1923 29509 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→34.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1361 0 0 130 1491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071401
X-RAY DIFFRACTIONf_angle_d0.9121853
X-RAY DIFFRACTIONf_dihedral_angle_d12.742513
X-RAY DIFFRACTIONf_chiral_restr0.041213
X-RAY DIFFRACTIONf_plane_restr0.004223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65170.22941160.17832509X-RAY DIFFRACTION99
1.6517-1.71070.20031250.18672518X-RAY DIFFRACTION99
1.7107-1.77920.20661390.18382362X-RAY DIFFRACTION94
1.7792-1.86020.20431290.17992522X-RAY DIFFRACTION98
1.8602-1.95820.23151400.18012553X-RAY DIFFRACTION99
1.9582-2.08090.2061530.18122536X-RAY DIFFRACTION99
2.0809-2.24150.20481260.16762576X-RAY DIFFRACTION99
2.2415-2.4670.19931340.18272525X-RAY DIFFRACTION97
2.467-2.82390.22051510.19482523X-RAY DIFFRACTION97
2.8239-3.55720.19781510.2052651X-RAY DIFFRACTION100
3.5572-34.10570.21011320.20432738X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4686-0.2361-1.74250.5697-0.0296.98090.1179-0.16210.13690.02530.0599-0.0213-0.14970.7782-0.07440.0626-0.00250.0160.1184-0.00610.1435-2.6031-14.7671-22.1627
21.3904-0.6251-1.62831.52660.96426.0607-0.0803-0.07760.01470.10330.1043-0.05220.76350.40260.07980.08480.0327-0.00110.0891-0.0190.1343-5.811-23.0921-21.9719
31.53290.3458-0.42480.9396-0.29691.83480.15380.00970.17580.09420.0003-0.0003-0.60950.4381-0.03160.11790.00470.02180.06650.01520.1461-7.8741-7.6207-23.2021
41.4713-0.3498-0.25920.81240.55466.62420.1126-0.0423-0.0743-0.0051-0.07570.11570.0743-0.84850.03040.065-0.0097-0.0130.1522-0.00090.1648-20.3752-16.8889-23.4977
51.1831-0.18830.71161.0429-0.16061.63240.1067-0.03390.00310.00070.0675-0.032-0.6051-0.3219-0.03320.09750.0446-0.0030.10310.01050.1188-16.9704-8.6197-24.4738
62.12050.0218-0.47551.67410.64142.17270.06740.1698-0.06540.0635-0.0040.01230.5818-0.49420.11930.116-0.0134-0.01780.09-0.01950.1466-14.7957-24.1119-22.7672
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:30)
2X-RAY DIFFRACTION2CHAIN B AND (RESID 1:30)
3X-RAY DIFFRACTION3CHAIN C AND (RESID 1:30)
4X-RAY DIFFRACTION4CHAIN E AND (RESID 1:30)
5X-RAY DIFFRACTION5CHAIN F AND (RESID 1:30)
6X-RAY DIFFRACTION6CHAIN D AND (RESID 1:31)

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