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- PDB-1tgg: RH3 DESIGNED RIGHT-HANDED COILED COIL TRIMER -

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Basic information

Entry
Database: PDB / ID: 1tgg
TitleRH3 DESIGNED RIGHT-HANDED COILED COIL TRIMER
Componentsright-handed coiled coil trimer
KeywordsDE NOVO PROTEIN / coiled coil / de novo design
Function / homologyNICKEL (II) ION
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsPlecs, J.J. / Harbury, P.B. / Kim, P.S. / Alber, T.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Structural test of the parameterized-backbone method for protein design
Authors: Plecs, J.J. / Harbury, P.B. / Kim, P.S. / Alber, T.
#1: Journal: Science / Year: 1998
Title: High-Resolution Design with Backbone Freedom
Authors: Harbury, P.B. / Plecs, J.J. / Tidor, B. / Alber, T. / Kim, P.S.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Repacking Protein Cores with Backbone Freedom: Structure Prediction for Coiled Coils
Authors: Harbury, P.B. / Tidor, B. / Kim, P.S.
History
DepositionMay 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: right-handed coiled coil trimer
B: right-handed coiled coil trimer
C: right-handed coiled coil trimer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,58111
Polymers12,2273
Non-polymers3538
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-73 kcal/mol
Surface area7180 Å2
MethodPISA
2
B: right-handed coiled coil trimer
hetero molecules

A: right-handed coiled coil trimer

C: right-handed coiled coil trimer


Theoretical massNumber of molelcules
Total (without water)12,58111
Polymers12,2273
Non-polymers3538
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3290 Å2
ΔGint-91 kcal/mol
Surface area8410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.42, 25.42, 141.34
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Cell settingtrigonal
Space group name H-MP32

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Components

#1: Protein/peptide right-handed coiled coil trimer


Mass: 4075.822 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: chemical peptide synthesis
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1.98 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris pH 8.5, 0.3M NaBr, 15mM NiCl2, 15% methyl pentanediol, 15% polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.4862, 1.4851, 1.3931
DetectorDetector: AREA DETECTOR
RadiationMonochromator: crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.48621
21.48511
31.39311
ReflectionResolution: 2→12 Å / Num. all: 11956 / Num. obs: 11956

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
X-PLOR3.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→12 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.269 1085 random
Rwork0.233 --
all0.236 11956 -
obs0.236 11956 -
Refinement stepCycle: LAST / Resolution: 2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms997 0 8 115 1120

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