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- PDB-3r3k: Crystal structure of a parallel 6-helix coiled coil -

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Basic information

Entry
Database: PDB / ID: 3r3k
TitleCrystal structure of a parallel 6-helix coiled coil
ComponentsCChex-Phi22 helix
KeywordsDE NOVO PROTEIN / parallel hexamer / KIH interactions / hydrophobic channel / synthetic biology
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2009 Å
AuthorsZaccai, N.R. / Chi, B.H.C. / Woolfson, D.N. / Brady, R.L.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: A de novo peptide hexamer with a mutable channel.
Authors: Zaccai, N.R. / Chi, B. / Thomson, A.R. / Boyle, A.L. / Bartlett, G.J. / Bruning, M. / Linden, N. / Sessions, R.B. / Booth, P.J. / Brady, R.L. / Woolfson, D.N.
History
DepositionMar 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: 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_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: CChex-Phi22 helix
B: CChex-Phi22 helix
C: CChex-Phi22 helix
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,72111
Polymers10,4343
Non-polymers2878
Water1,27971
1
A: CChex-Phi22 helix
B: CChex-Phi22 helix
C: CChex-Phi22 helix
hetero molecules

A: CChex-Phi22 helix
B: CChex-Phi22 helix
C: CChex-Phi22 helix
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,44122
Polymers20,8676
Non-polymers57416
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area9180 Å2
ΔGint-96 kcal/mol
Surface area9860 Å2
MethodPISA
2
A: CChex-Phi22 helix
B: CChex-Phi22 helix
C: CChex-Phi22 helix
hetero molecules

A: CChex-Phi22 helix
B: CChex-Phi22 helix
C: CChex-Phi22 helix
hetero molecules

A: CChex-Phi22 helix
B: CChex-Phi22 helix
C: CChex-Phi22 helix
hetero molecules

A: CChex-Phi22 helix
B: CChex-Phi22 helix
C: CChex-Phi22 helix
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,88344
Polymers41,73512
Non-polymers1,14832
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area21340 Å2
ΔGint-212 kcal/mol
Surface area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.660, 54.480, 128.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-45-

HOH

21B-74-

HOH

31B-84-

HOH

41C-42-

HOH

51C-65-

HOH

61C-72-

HOH

71C-88-

HOH

81C-89-

HOH

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Components

#1: Protein/peptide CChex-Phi22 helix


Mass: 3477.891 Da / Num. of mol.: 3 / Fragment: helix from coiled coil domain / Source method: obtained synthetically
Details: Peptide synthesis carried out according to standard Fmoc SPPS protocols
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 mM sodium L-glutamate, 20 mM alanine (racemic), 20 mM glycine, 20 mM lysine hydrochloride (racemic), 20 mM serine (racemic), 50 mM sodium HEPES, 50 mM MOPS (acid) pH 7.5, 20 % ethylene ...Details: 20 mM sodium L-glutamate, 20 mM alanine (racemic), 20 mM glycine, 20 mM lysine hydrochloride (racemic), 20 mM serine (racemic), 50 mM sodium HEPES, 50 mM MOPS (acid) pH 7.5, 20 % ethylene glycol,10 % PEG 8K, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.7 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.2→50.14 Å / Num. obs: 5716 / % possible obs: 95.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 9.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 2.2 / % possible all: 72.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2009→23.21 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 24.86 / Stereochemistry target values: ML
Details: F(+) and F(-) treated separately during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2715 472 4.64 %RANDOM
Rwork0.2124 ---
obs0.2153 10181 93.46 %-
all-10181 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.818 Å2 / ksol: 0.406 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2927 Å2-0 Å2-0 Å2
2---2.2866 Å20 Å2
3----5.3988 Å2
Refinement stepCycle: LAST / Resolution: 2.2009→23.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms678 0 14 71 763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015705
X-RAY DIFFRACTIONf_angle_d1.285927
X-RAY DIFFRACTIONf_dihedral_angle_d21.327273
X-RAY DIFFRACTIONf_chiral_restr0.098111
X-RAY DIFFRACTIONf_plane_restr0.004113
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2009-2.5190.23181310.21382787X-RAY DIFFRACTION81
2.519-3.17240.31151730.19093475X-RAY DIFFRACTION100
3.1724-23.21080.26021680.22573447X-RAY DIFFRACTION100

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