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- PDB-4kvu: Crystal structure of a 6-helix coiled coil CC-Hex-L17C-W224BF -

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Basic information

Entry
Database: PDB / ID: 4kvu
TitleCrystal structure of a 6-helix coiled coil CC-Hex-L17C-W224BF
Components6-helix coiled coil CC-Hex-L17C-W224BF
KeywordsDE NOVO PROTEIN / De Novo Coiled-coil assembly
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-helix coiled coil CC-Hex-L17C-W224BF
B: 6-helix coiled coil CC-Hex-L17C-W224BF
C: 6-helix coiled coil CC-Hex-L17C-W224BF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2774
Polymers10,1853
Non-polymers921
Water1,24369
1
A: 6-helix coiled coil CC-Hex-L17C-W224BF
B: 6-helix coiled coil CC-Hex-L17C-W224BF
C: 6-helix coiled coil CC-Hex-L17C-W224BF
hetero molecules

A: 6-helix coiled coil CC-Hex-L17C-W224BF
B: 6-helix coiled coil CC-Hex-L17C-W224BF
C: 6-helix coiled coil CC-Hex-L17C-W224BF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5538
Polymers20,3696
Non-polymers1842
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area9110 Å2
ΔGint-106 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.010, 60.980, 125.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11C-2-

GLU

21A-101-

GOL

31A-101-

GOL

41A-203-

HOH

51A-208-

HOH

61A-218-

HOH

71A-219-

HOH

81A-220-

HOH

91B-109-

HOH

101B-110-

HOH

111B-111-

HOH

121B-112-

HOH

131B-122-

HOH

141C-103-

HOH

151C-113-

HOH

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Components

#1: Protein/peptide 6-helix coiled coil CC-Hex-L17C-W224BF


Mass: 3394.838 Da / Num. of mol.: 3 / Source method: obtained synthetically
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M MOPS, 0.1 M magnesium acetate with 12 % w/v PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 68 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 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: 1.8→31.36 Å / Num. obs: 19390 / % possible obs: 100 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 2.7

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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: 1.8→30.695 Å / SU ML: 0.16 / σ(F): 0.12 / Phase error: 22.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2158 927 4.78 %
Rwork0.1944 --
obs0.1954 19055 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→30.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms650 0 6 69 725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008657
X-RAY DIFFRACTIONf_angle_d1.017855
X-RAY DIFFRACTIONf_dihedral_angle_d14.38242
X-RAY DIFFRACTIONf_chiral_restr0.039103
X-RAY DIFFRACTIONf_plane_restr0.003103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8950.25191470.25852614X-RAY DIFFRACTION99
1.895-2.01370.22291240.21552647X-RAY DIFFRACTION99
2.0137-2.16910.21191480.19512628X-RAY DIFFRACTION99
2.1691-2.38730.1531230.16462644X-RAY DIFFRACTION99
2.3873-2.73260.1941270.18962627X-RAY DIFFRACTION98
2.7326-3.44210.2411240.19982680X-RAY DIFFRACTION100
3.4421-31.36470.231340.18882623X-RAY DIFFRACTION98
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)
10.9869-0.7242-0.45661.6888-0.59532.9668-0.07150.0072-0.0979-0.0767-0.03890.01620.8430.11090.12480.1432-0.0197-0.0040.09490.01620.1981-26.73-9.012323.036
21.7230.1886-0.12150.9711-1.82794.4280.0930.059-0.0481-0.0352-0.0887-0.03160.16970.94680.05840.11350.0324-0.01150.15110.0160.2333-19.8025-3.146223.1464
31.93590.22732.15081.0839-0.17342.5588-0.10590.16610.06290.03870.031-0.0174-0.74340.5370.16730.1249-0.0344-0.01250.15530.00620.2118-21.73086.255821.6118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1 : 29 )
2X-RAY DIFFRACTION2CHAIN B AND (RESID 1 : 30 )
3X-RAY DIFFRACTION3CHAIN C AND (RESID 1 : 27 )

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