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- PDB-3twg: Crystal structure of the de novo designed fluorinated peptide alp... -

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Basic information

Entry
Database: PDB / ID: 3twg
TitleCrystal structure of the de novo designed fluorinated peptide alpha4F3af3d
Componentsalpha4F3af3d
KeywordsUNKNOWN FUNCTION / alpha helix / de novo designed / fluorinated protein
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsBuer, B.C. / Meagher, J.L. / Stuckey, J.A. / Marsh, E.N.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis for the enhanced stability of highly fluorinated proteins.
Authors: Buer, B.C. / Meagher, J.L. / Stuckey, J.A. / Marsh, E.N.
History
DepositionSep 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Mar 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alpha4F3af3d
B: alpha4F3af3d


Theoretical massNumber of molelcules
Total (without water)7,3372
Polymers7,3372
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: alpha4F3af3d
B: alpha4F3af3d

A: alpha4F3af3d
B: alpha4F3af3d


Theoretical massNumber of molelcules
Total (without water)14,6734
Polymers14,6734
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
3
A: alpha4F3af3d


Theoretical massNumber of molelcules
Total (without water)3,6681
Polymers3,6681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: alpha4F3af3d


Theoretical massNumber of molelcules
Total (without water)3,6681
Polymers3,6681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.956, 36.363, 41.457
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-35-

HOH

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Components

#1: Protein/peptide alpha4F3af3d


Mass: 3668.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 1.83 Å3/Da / Density % sol: 32.65 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
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-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 11, 2011
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. all: 5317 / Num. obs: 5280 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 10.3 % / Rmerge(I) obs: 0.046 / Χ2: 0.816 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.72-1.7510.70.5232430.4861100
1.75-1.7810.60.4252620.471100
1.78-1.8210.70.3582650.4961100
1.82-1.8510.60.272550.4891100
1.85-1.8910.70.232540.5211100
1.89-1.9410.70.1752610.5171100
1.94-1.9910.50.1272640.6071100
1.99-2.0410.90.1162620.621100
2.04-2.110.50.0862500.6731100
2.1-2.1710.70.0712700.8111100
2.17-2.2410.70.0622591.0591100
2.24-2.3310.60.0562651.0371100
2.33-2.4410.40.0562641.1431100
2.44-2.5710.60.0592621.1191100
2.57-2.7310.20.0592631.1181100
2.73-2.94100.0572681.1761100
2.94-3.249.60.0532760.9441100
3.24-3.719.80.0392780.9811100
3.71-4.679.40.0352791.118198.9
4.67-5080.0342801.01189.5

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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_EXTRACT3.1data extraction
MD2data collection
HKL-2000data reduction
HKL-2000data scaling
BUSTER1.6.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→9.08 Å / Cor.coef. Fo:Fc: 0.9316 / Cor.coef. Fo:Fc free: 0.9254 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.2898 239 4.57 %RANDOM
Rwork0.2413 ---
obs0.2437 5229 --
Displacement parametersBiso max: 119.58 Å2 / Biso mean: 45.824 Å2 / Biso min: 21.59 Å2
Baniso -1Baniso -2Baniso -3
1-1.5418 Å20 Å20 Å2
2--1.6988 Å20 Å2
3----3.2407 Å2
Refine analyzeLuzzati coordinate error obs: 0.343 Å
Refinement stepCycle: LAST / Resolution: 1.72→9.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms433 0 0 19 452
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d157SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes14HARMONIC2
X-RAY DIFFRACTIONt_gen_planes62HARMONIC5
X-RAY DIFFRACTIONt_it462HARMONIC20
X-RAY DIFFRACTIONt_nbd26SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion36SEMIHARMONIC5
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_contact409SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d462HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg654HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion1.83
X-RAY DIFFRACTIONt_other_torsion17.12
LS refinement shellResolution: 1.72→1.92 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.302 77 5.3 %
Rwork0.2416 1376 -
all0.2448 1453 -
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)
18.0676-1.8714-0.17747.66592.59315.26360.1604-0.0032-0.1583-0.15420.02230.21580.1910.0827-0.1827-0.10680.0308-0.0083-0.03120.0260.014-6.83120.0711-3.3089
26.13492.1830.5534.71730.95058.3155-0.0950.27960.1065-0.52920.1683-0.20090.17460.0808-0.0733-0.02730.00310.0808-0.13710.0298-0.0088-0.96176.9567-4.3834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|5 - A|26 }A5 - 26
2X-RAY DIFFRACTION2{ B|1 - B|25 }B1 - 25

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