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- PDB-6trk: Phl p 6 fold stabilized mutant - S46Y -

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Basic information

Entry
Database: PDB / ID: 6trk
TitlePhl p 6 fold stabilized mutant - S46Y
ComponentsPollen allergen Phl p 6
KeywordsALLERGEN / Phleum pratense / grass pollen allergen / stabilized fold mutant / Phl p 6
Function / homologyPollen allergen Poa p IX/Phl p VI / Pollen allergen/Uncharacterized protein Os / Ribonuclease (pollen allergen) / Pollen allergen Phl p 6
Function and homology information
Biological speciesPhleum pratense (timothy grass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSoh, W.T. / Brandstetter, H.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundW_01213 Austria
Citation
Journal: Front Immunol / Year: 2020
Title: In silico Design of Phl p 6 Variants With Altered Fold-Stability Significantly Impacts Antigen Processing, Immunogenicity and Immune Polarization.
Authors: Winter, P. / Stubenvoll, S. / Scheiblhofer, S. / Joubert, I.A. / Strasser, L. / Briganser, C. / Soh, W.T. / Hofer, F. / Kamenik, A.S. / Dietrich, V. / Michelini, S. / Laimer, J. / Lackner, P. ...Authors: Winter, P. / Stubenvoll, S. / Scheiblhofer, S. / Joubert, I.A. / Strasser, L. / Briganser, C. / Soh, W.T. / Hofer, F. / Kamenik, A.S. / Dietrich, V. / Michelini, S. / Laimer, J. / Lackner, P. / Horejs-Hoeck, J. / Tollinger, M. / Liedl, K.R. / Brandstetter, J. / Huber, C.G. / Weiss, R.
#1: Journal: Biorxiv / Year: 2020
Title: In silico design of Phl p 6 variants with altered folding stability significantly impacts antigen processing, immunogenicity and immune polarization
Authors: Winter, P. / Stubenvoll, S. / Scheiblhofer, S. / Joubert, I.A. / Strasser, L. / Briganser, C. / Soh, W.T. / Hofer, F. / Kamenik, A.S. / Dietrich, V. / Michelini, S. / Laimer, J. / Lackner, P. ...Authors: Winter, P. / Stubenvoll, S. / Scheiblhofer, S. / Joubert, I.A. / Strasser, L. / Briganser, C. / Soh, W.T. / Hofer, F. / Kamenik, A.S. / Dietrich, V. / Michelini, S. / Laimer, J. / Lackner, P. / Horejs-Hoeck, J. / Tollinger, M. / Liedl, K.R. / Brandstetter, H. / Huber, C.G. / Weiss, R.
History
DepositionDec 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pollen allergen Phl p 6
B: Pollen allergen Phl p 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0246
Polymers23,7632
Non-polymers2624
Water6,990388
1
A: Pollen allergen Phl p 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0784
Polymers11,8811
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pollen allergen Phl p 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9472
Polymers11,8811
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.825, 73.515, 76.124
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-515-

HOH

21B-316-

HOH

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Components

#1: Protein Pollen allergen Phl p 6 / Allergen Phl p VI


Mass: 11881.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phleum pratense (timothy grass) / Gene: PHLPVI / Production host: Escherichia coli (E. coli) / References: UniProt: P43215
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.86 Å3/Da / Density % sol: 56.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 50 mM Zinc acetate dehydrate, 10% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→39.94 Å / Num. obs: 34555 / % possible obs: 96.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 16.9 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5013 / CC1/2: 0.778 / % possible all: 97.5

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Processing

Software
NameVersionClassification
iMOSFLMdata processing
PHENIX1.17_3644refinement
SCALAdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NLX

1nlx


Resolution: 1.6→33.8 Å / SU ML: 0.1615 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.1598
RfactorNum. reflection% reflection
Rfree0.1877 1723 5 %
Rwork0.1556 --
obs0.1571 34481 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.03 Å2
Refinement stepCycle: LAST / Resolution: 1.6→33.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1651 0 4 388 2043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00891817
X-RAY DIFFRACTIONf_angle_d0.9932490
X-RAY DIFFRACTIONf_chiral_restr0.0538277
X-RAY DIFFRACTIONf_plane_restr0.0074332
X-RAY DIFFRACTIONf_dihedral_angle_d24.0248672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.30861630.24192657X-RAY DIFFRACTION95.95
1.65-1.710.21441430.2172723X-RAY DIFFRACTION96.99
1.71-1.770.24081510.19352748X-RAY DIFFRACTION98.64
1.77-1.840.22771500.19082730X-RAY DIFFRACTION97.69
1.84-1.920.20591470.18232722X-RAY DIFFRACTION97.65
1.92-2.020.18581520.16772686X-RAY DIFFRACTION96.6
2.02-2.150.20181220.15172756X-RAY DIFFRACTION96.09
2.15-2.310.16651450.14012743X-RAY DIFFRACTION97.27
2.31-2.550.15521330.13862757X-RAY DIFFRACTION96.46
2.55-2.920.16491400.14492703X-RAY DIFFRACTION94.58
2.92-3.670.20091220.13972750X-RAY DIFFRACTION94.35
3.67-33.80.17031550.14812783X-RAY DIFFRACTION92.33
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)
10.214887198562-0.224673794364-0.07982803183620.3562522904820.2655259519250.305170519733-0.007501081071820.0258277815595-0.0448823529091-0.006303824320180.0201198708986-0.09859328741850.00935749604928-0.06959432862720.003927653110020.0447723368317-0.0172248612082-0.001592538650120.0560703485955-0.006923972866420.065744295937421.808701371276.257388752822.0298991423
20.2697478443080.292090368521-0.243065430440.495775347251-0.2521207425830.3032733523570.1051784079890.02656913850260.09281569540410.283164298668-0.01918836606910.185366234726-0.106080007428-0.02005068838130.1031856843750.1437615180110.01126300095440.03814080629850.09049848955830.01085425233390.1046467103314.738451144396.979605210430.9074389737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A
2X-RAY DIFFRACTION2Chain B

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