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- PDB-4g4m: Crystal structure of the de novo designed fluorinated peptide alp... -

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Basic information

Entry
Database: PDB / ID: 4g4m
TitleCrystal structure of the de novo designed fluorinated peptide alpha4F3(6-13)
Componentsalpha4F3(6-13)
KeywordsDE NOVO PROTEIN / alpha helix / de novo designed / fluorinated protein / coiled-coil
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsBuer, B.C. / Meagher, J.L. / Stuckey, J.A. / Marsh, E.N.G.
CitationJournal: Protein Sci. / Year: 2012
Title: Comparison of the structures and stabilities of coiled-coil proteins containing hexafluoroleucine and t-butylalanine provides insight into the stabilizing effects of highly fluorinated amino acid side-chains.
Authors: Buer, B.C. / Meagher, J.L. / Stuckey, J.A. / Marsh, E.N.
History
DepositionJul 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alpha4F3(6-13)
B: alpha4F3(6-13)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7567
Polymers7,1812
Non-polymers5755
Water50428
1
A: alpha4F3(6-13)
B: alpha4F3(6-13)
hetero molecules

A: alpha4F3(6-13)
B: alpha4F3(6-13)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,51214
Polymers14,3624
Non-polymers1,14910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Unit cell
Length a, b, c (Å)49.581, 49.581, 41.569
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein/peptide alpha4F3(6-13)


Mass: 3590.581 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 1.78 Å3/Da / Density % sol: 30.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 48% PEG600, 0.1M Tris pH 8.5, vapor diffusion, hanging drop, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 2011
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 8484

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
BUSTER1.6.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→10 Å / Cor.coef. Fo:Fc: 0.9152 / Cor.coef. Fo:Fc free: 0.8716 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3176 394 4.66 %RANDOM
Rwork0.2522 ---
obs0.2553 8457 --
Displacement parametersBiso max: 84.26 Å2 / Biso mean: 30.4037 Å2 / Biso min: 12.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.0565 Å20 Å20 Å2
2---1.0565 Å20 Å2
3---2.113 Å2
Refine analyzeLuzzati coordinate error obs: 0.291 Å
Refinement stepCycle: LAST / Resolution: 1.48→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms468 0 26 28 522
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d174SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes16HARMONIC2
X-RAY DIFFRACTIONt_gen_planes58HARMONIC5
X-RAY DIFFRACTIONt_it489HARMONIC20
X-RAY DIFFRACTIONt_nbd25SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion42SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact524SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d489HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg656HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion19.34
LS refinement shellResolution: 1.48→1.66 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2963 103 4.29 %
Rwork0.2603 2297 -
all0.2619 2400 -
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)
13.70640.9509-2.25633.1665-1.63559.5236-0.01280.06940.10520.14220.0797-0.0862-0.0523-0.1492-0.0668-0.0605-0.0037-0.0153-0.04540.0404-0.04985.3005-5.3552-18.1618
25.3922-0.6502-4.28173.45780.0432.8773-0.0045-0.03290.0490.0208-0.02110.015-0.04280.04570.0256-0.01070.0184-0.0189-0.0721-0.0155-0.0697-4.2049-5.7823-13.6684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 25
2X-RAY DIFFRACTION2{ B|* }B1 - 25

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