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- PDB-4g4l: Crystal structure of the de novo designed peptide alpha4tbA6 -

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Basic information

Entry
Database: PDB / ID: 4g4l
TitleCrystal structure of the de novo designed peptide alpha4tbA6
Componentsalpha4tbA6
KeywordsDE NOVO PROTEIN / alpha helix / de novo designed / coiled-coil / nonnatural amino acid
Function / homologyACETYL GROUP / DI(HYDROXYETHYL)ETHER
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 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
Revision 1.3Mar 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alpha4tbA6
B: alpha4tbA6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1345
Polymers6,7022
Non-polymers4333
Water55831
1
A: alpha4tbA6
B: alpha4tbA6
hetero molecules

A: alpha4tbA6
B: alpha4tbA6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,26910
Polymers13,4044
Non-polymers8656
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
2
B: alpha4tbA6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5013
Polymers3,3511
Non-polymers1502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: alpha4tbA6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6332
Polymers3,3511
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.307, 37.417, 40.761
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein/peptide alpha4tbA6


Mass: 3350.914 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 1.78 Å3/Da / Density % sol: 30.94 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 48% PEG400, 0.1M HEPES pH 9.0, 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: Nov 30, 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: 1.48→50 Å / Num. obs: 7348

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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
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
BUSTER1.6.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→27.56 Å / Cor.coef. Fo:Fc: 0.9243 / Cor.coef. Fo:Fc free: 0.9321 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2447 337 4.59 %RANDOM
Rwork0.2415 ---
obs0.2416 7348 --
Displacement parametersBiso max: 120.56 Å2 / Biso mean: 37.9767 Å2 / Biso min: 18.39 Å2
Baniso -1Baniso -2Baniso -3
1--5.1073 Å20 Å20 Å2
2--3.9926 Å20 Å2
3---1.1146 Å2
Refine analyzeLuzzati coordinate error obs: 0.241 Å
Refinement stepCycle: LAST / Resolution: 1.54→27.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms429 0 26 31 486
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d150SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes16HARMONIC2
X-RAY DIFFRACTIONt_gen_planes56HARMONIC5
X-RAY DIFFRACTIONt_it453HARMONIC20
X-RAY DIFFRACTIONt_nbd
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_contact491SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d453HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg609HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion1.68
X-RAY DIFFRACTIONt_other_torsion18.01
LS refinement shellResolution: 1.54→1.72 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.221 80 3.99 %
Rwork0.1929 1923 -
all0.194 2003 -
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)
14.82661.51981.3534.0892-0.70644.07590.047-0.18750.2160.0496-0.15180.3496-0.012-0.20250.1048-0.0506-0.00790.0143-0.0247-0.03380.0006-7.9093-0.51556.4691
23.6499-0.8196-2.46963.7721.77647.75970.0481-0.1554-0.28350.1274-0.10920.06580.14760.17360.0612-0.0823-0.01380.0021-0.0690.0136-0.0408-0.8427-8.09223.9112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 25
2X-RAY DIFFRACTION2{ B|* }B1 - 27

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