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- PDB-4onk: [Leu-5]-Enkephalin mutant - YVVFL -

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Basic information

Entry
Database: PDB / ID: 4onk
Title[Leu-5]-Enkephalin mutant - YVVFL
Components[Leu-5]-Enkephalin mutant - YVVFL
KeywordsPROTEIN FIBRIL / amyloid-like protofibril
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSangwan, S. / Eisenberg, D. / Sawaya, M.R. / Do, T.D. / Bowers, M.T. / Lapointe, N.E. / Teplow, D.B. / Feinstein, S.C.
CitationJournal: J.Phys.Chem.B / Year: 2014
Title: Factors that drive Peptide assembly from native to amyloid structures: experimental and theoretical analysis of [leu-5]-enkephalin mutants.
Authors: Do, T.D. / LaPointe, N.E. / Sangwan, S. / Teplow, D.B. / Feinstein, S.C. / Sawaya, M.R. / Eisenberg, D.S. / Bowers, M.T.
History
DepositionJan 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: [Leu-5]-Enkephalin mutant - YVVFL
B: [Leu-5]-Enkephalin mutant - YVVFL


Theoretical massNumber of molelcules
Total (without water)1,2802
Polymers1,2802
Non-polymers00
Water543
1
A: [Leu-5]-Enkephalin mutant - YVVFL
B: [Leu-5]-Enkephalin mutant - YVVFL
x 6


Theoretical massNumber of molelcules
Total (without water)7,67712
Polymers7,67712
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_665x+1,y+1,z1
crystal symmetry operation1_765x+2,y+1,z1
Unit cell
Length a, b, c (Å)9.613, 13.827, 14.835
Angle α, β, γ (deg.)90.610, 103.120, 108.300
Int Tables number1
Space group name H-MP1
DetailsThe biological unit is a pair of beta sheets. One sheet is constructed from chains A and B with unit cell translations along the a direction (i.e. X+1,Y,Z; X+2,Y,Z; X+3,Y,Z, etc.). The second sheet is constructed from X,Y+1,Z; X+1,Y+1,Z; X+2,Y+1,Z; etc.).

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Components

#1: Protein/peptide [Leu-5]-Enkephalin mutant - YVVFL


Mass: 639.782 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: reservoir contained 25% PEG 3350, 0.2M Potassium Thiocyanate, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. all: 537 / Num. obs: 537 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 8.11 Å2 / Rmerge(I) obs: 0.151 / Χ2: 3.634 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.973.40.153501.927190.9
1.97-2.053.30.216545.114198.2
2.05-2.143.90.16513.341100
2.14-2.253.80.195583.0941100
2.25-2.393.70.182602.323193.8
2.39-2.583.90.148462.5091100
2.58-2.843.90.157552.561194.8
2.84-3.253.90.152594.4021100
3.25-4.093.80.147506.223198
4.09-1004.60.123544.655194.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.9 Å9.28 Å
Translation1.9 Å9.28 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.2phasing
PHENIXdev_1457refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ideal beta strand with sequence AVVAA

Resolution: 1.9→9.278 Å / FOM work R set: 0.8404 / SU ML: 0.29 / σ(F): 35.13 / Phase error: 23.66 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 47 9 %RANDOM
Rwork0.1513 ---
all0.1549 522 --
obs0.1549 522 93.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 22.76 Å2 / Biso mean: 14.15 Å2 / Biso min: 8.29 Å2
Refinement stepCycle: LAST / Resolution: 1.9→9.278 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms92 0 0 3 95
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00694
X-RAY DIFFRACTIONf_angle_d0.842128
X-RAY DIFFRACTIONf_chiral_restr0.03916
X-RAY DIFFRACTIONf_plane_restr0.00614
X-RAY DIFFRACTIONf_dihedral_angle_d10.95228
LS refinement shellHighest resolution: 1.9003 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.1994 47 -
Rwork0.1513 475 -
all-522 -
obs--94 %

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