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- PDB-4g3b: Crystal structure of the de novo designed fluorinated peptide alp... -

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Basic information

Entry
Database: PDB / ID: 4g3b
TitleCrystal structure of the de novo designed fluorinated peptide alpha4F3d
Componentsalpha4F3d
KeywordsDE NOVO PROTEIN / alpha helix / de novo designed / fluorinated protein / coiled-coil
Function / homologyACETYL GROUP
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.19 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 13, 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

Downloads & links

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Assembly

Deposited unit
A: alpha4F3d
B: alpha4F3d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1113
Polymers7,0672
Non-polymers441
Water88349
1
A: alpha4F3d
B: alpha4F3d
hetero molecules

A: alpha4F3d
B: alpha4F3d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2226
Polymers14,1344
Non-polymers882
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-8 kcal/mol
Surface area4740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.819, 39.251, 41.233
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operationsi: -x-1, -y, z

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Components

#1: Protein/peptide alpha4F3d


Mass: 3533.529 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized
#2: Chemical ChemComp-ACE / ACETYL GROUP / Acetyl group


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 1.76 Å3/Da / Density % sol: 30.29 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 55% PEG400, 0.1M Tris pH 7.8, 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-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 2, 2012
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.19→50 Å / Num. obs: 16392

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.11data extraction
MD2data collection
HKL-2000data reduction
HKL-2000data scaling
BUSTER1.6.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→11.16 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.9355 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1872 831 5.07 %RANDOM
Rwork0.1777 ---
obs0.1782 16392 --
Displacement parametersBiso max: 75.77 Å2 / Biso mean: 15.5709 Å2 / Biso min: 5.53 Å2
Baniso -1Baniso -2Baniso -3
1--1.5063 Å20 Å20 Å2
2--1.0122 Å20 Å2
3---0.494 Å2
Refine analyzeLuzzati coordinate error obs: 0.127 Å
Refinement stepCycle: LAST / Resolution: 1.19→11.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms482 0 3 49 534
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d193SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes18HARMONIC2
X-RAY DIFFRACTIONt_gen_planes68HARMONIC5
X-RAY DIFFRACTIONt_it520HARMONIC20
X-RAY DIFFRACTIONt_nbd12SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion46SEMIHARMONIC5
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_contact575SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d520HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg717HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion2.27
X-RAY DIFFRACTIONt_other_torsion12.4
LS refinement shellResolution: 1.19→1.27 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.1587 161 5.64 %
Rwork0.1376 2696 -
all0.1388 2857 -
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)
11.3839-0.04670.15732.3805-1.37183.1191-0.00670.06660.0591-0.0726-0.0439-0.0590.00420.08840.0506-0.02560.0043-0.004-0.0330.0044-0.0044-8.0006-0.637214.9524
21.32240.3657-0.69921.2428-0.3644.1336-0.01590.0531-0.0121-0.0365-0.01830.01260.0946-0.01030.0342-0.02340.00440.0003-0.0278-0.0065-0.0005-14.8816-7.277817.494
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|26 }A1 - 26
2X-RAY DIFFRACTION2{ B|1 - B|26 }B1 - 26

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