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- PDB-1u9g: Heterocyclic Peptide Backbone Modification in GCN4-pLI Based Coil... -

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Basic information

Entry
Database: PDB / ID: 1u9g
TitleHeterocyclic Peptide Backbone Modification in GCN4-pLI Based Coiled Coils: Replacement of K(8)L(9)
ComponentsGeneral control protein GCN4
KeywordsTRANSCRIPTION / tetrameric alpha-helical coiled coil with heteerocycic backbone modification
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHorne, W.S. / Yadav, M.K. / Stout, C.D. / Ghadiri, M.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2004
Title: Heterocyclic peptide backbone modifications in an alpha-helical coiled coil.
Authors: Horne, W.S. / Yadav, M.K. / Stout, C.D. / Ghadiri, M.R.
History
DepositionAug 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: General control protein GCN4
B: General control protein GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0933
Polymers7,9972
Non-polymers961
Water34219
1
A: General control protein GCN4
B: General control protein GCN4
hetero molecules

A: General control protein GCN4
B: General control protein GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1876
Polymers15,9954
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_554z+1/4,-y+1/4,x-1/41
Buried area4560 Å2
ΔGint-49 kcal/mol
Surface area4930 Å2
MethodPISA, PQS
2
B: General control protein GCN4
hetero molecules

B: General control protein GCN4
hetero molecules

B: General control protein GCN4
hetero molecules

A: General control protein GCN4

A: General control protein GCN4

A: General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)24,2809
Polymers23,9926
Non-polymers2883
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
crystal symmetry operation15_554y+1/4,-x+1/4,z-1/41
crystal symmetry operation20_554x+1/4,-z+1/4,y-1/41
crystal symmetry operation22_554z+1/4,-y+1/4,x-1/41
Buried area5780 Å2
ΔGint-103 kcal/mol
Surface area9000 Å2
MethodPISA
3
A: General control protein GCN4
B: General control protein GCN4
hetero molecules

A: General control protein GCN4
B: General control protein GCN4
hetero molecules

A: General control protein GCN4
B: General control protein GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2809
Polymers23,9926
Non-polymers2883
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area4350 Å2
ΔGint-89 kcal/mol
Surface area10430 Å2
MethodPISA
4
A: General control protein GCN4
B: General control protein GCN4
hetero molecules

A: General control protein GCN4
B: General control protein GCN4
hetero molecules

A: General control protein GCN4
B: General control protein GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2809
Polymers23,9926
Non-polymers2883
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area4110 Å2
ΔGint-88 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.228, 78.228, 78.228
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11B-1-

SO4

21B-1-

SO4

31A-38-

HOH

DetailsThe tetramer formed by chains A and B is generated by the two fold axis: 3/4+z,1/4+y,1/4-x

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Components

#1: Protein/peptide General control protein GCN4 / Amino acid biosynthesis regulatory protein


Mass: 3998.696 Da / Num. of mol.: 2 / Mutation: (TA4)9L, D8K / Source method: obtained synthetically
Details: Prepared by Fmoc solid phase peptide synthesis.The sequence of this protein can be found naturally in Saccharomyces cerevisiae (Baker's yeast).
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.4 M lithium sulfate monohydrate, 12% w/v PEG 8000, 20% v/v anhydrous glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 13, 2004 / Details: osmic confocal mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→45.17 Å / Num. obs: 4526 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 11
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 2.2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.17 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.882 / SU B: 6.689 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32575 208 4.6 %RANDOM
Rwork0.24477 ---
all0.24856 ---
obs0.24856 4295 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.59 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms363 0 5 19 387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021371
X-RAY DIFFRACTIONr_bond_other_d0.030.02360
X-RAY DIFFRACTIONr_angle_refined_deg2.6642.083501
X-RAY DIFFRACTIONr_angle_other_deg1.9793829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.456542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.2362615
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.7931567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.195151
X-RAY DIFFRACTIONr_chiral_restr0.0920.261
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02381
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0260
X-RAY DIFFRACTIONr_nbd_refined0.3230.286
X-RAY DIFFRACTIONr_nbd_other0.1890.2320
X-RAY DIFFRACTIONr_nbtor_refined0.2110.2159
X-RAY DIFFRACTIONr_nbtor_other0.1030.2215
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3050.29
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0140.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4070.212
X-RAY DIFFRACTIONr_mcbond_it1.7831.5231
X-RAY DIFFRACTIONr_mcbond_other10.1531.598
X-RAY DIFFRACTIONr_mcangle_it2.1472350
X-RAY DIFFRACTIONr_scbond_it3.2293158
X-RAY DIFFRACTIONr_scangle_it4.4294.5151
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 15 -
Rwork0.292 313 -
obs--99.39 %

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