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- PDB-7kyw: Crystal structure of timothy grass allergen Phl p 12.0101 reveals... -

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Basic information

Entry
Database: PDB / ID: 7kyw
TitleCrystal structure of timothy grass allergen Phl p 12.0101 reveals an unusual profilin dimer
ComponentsProfilin-1
KeywordsALLERGEN / grass allergy / profilin / Phleum pratense / pollen-food syndrome / oral allergy syndrome
Function / homology
Function and homology information


: / actin monomer binding / cell cortex / cytoskeleton
Similarity search - Function
Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily
Similarity search - Domain/homology
CITRIC ACID / Profilin-1
Similarity search - Component
Biological speciesPhleum pratense (timothy grass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsO'Malley, A. / Kapingidza, A.B. / Hyduke, N. / Dolamore, C. / Chruszcz, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)2R01AI077653-10A1 United States
CitationJournal: Acta Biochim.Pol. / Year: 2021
Title: Crystal structure of timothy grass allergen Phl p 12.0101 reveals an unusual profilin dimer.
Authors: O'Malley, A. / Kapingidza, A.B. / Hyduke, N. / Dolamore, C. / Kowal, K. / Chruszcz, M.
History
DepositionDec 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Profilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3682
Polymers14,1761
Non-polymers1921
Water28816
1
A: Profilin-1
hetero molecules

A: Profilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7374
Polymers28,3522
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area2280 Å2
ΔGint-2 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.344, 56.344, 94.379
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-314-

HOH

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Components

#1: Protein Profilin-1 / Allergen Phl p 11 / Pollen allergen Phl p 12


Mass: 14176.177 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phleum pratense (timothy grass) / Gene: PRO1, PHLPXI / Production host: Escherichia coli (E. coli) / References: UniProt: P35079
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: 0.5 M sodium citrate at pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 8119 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / CC1/2: 0.942 / CC star: 0.985 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.021 / Rrim(I) all: 0.066 / Rsym value: 0.054 / Net I/σ(I): 50.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 405 / CC1/2: 0.825 / CC star: 0.951 / Rpim(I) all: 0.238 / Rrim(I) all: 0.766 / Rsym value: 0.698 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FEF

5fef


Resolution: 2.3→33.94 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 395 4.9 %RANDOM
Rwork0.1972 ---
obs0.1997 7700 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 128.93 Å2 / Biso mean: 65.408 Å2 / Biso min: 41.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å2-0.44 Å2-0 Å2
2---0.88 Å20 Å2
3---2.85 Å2
Refinement stepCycle: final / Resolution: 2.3→33.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 13 16 1021
Biso mean--117.84 68.05 -
Num. residues----131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131036
X-RAY DIFFRACTIONr_bond_other_d0.0360.017960
X-RAY DIFFRACTIONr_angle_refined_deg1.491.6411402
X-RAY DIFFRACTIONr_angle_other_deg2.2941.5792226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2855132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.98824.1346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.915172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.655153
X-RAY DIFFRACTIONr_chiral_restr0.0740.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021192
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02214
LS refinement shellResolution: 2.301→2.361 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 29 -
Rwork0.302 556 -
all-585 -
obs--98.98 %
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)
13.5521-1.9796-1.07396.08680.29446.75490.12480.244-0.0399-0.1235-0.42590.06451.1895-0.27490.3010.45120.09930.0170.1218-0.0380.020525.933-8.04720.867
26.9646-0.14630.39255.83861.43794.32080.32011.0890.4779-0.7243-0.618-0.18950.02740.23360.2980.40250.25550.0910.30420.13150.067130.8212.4896.805
32.3999-1.59680.17643.7238-2.9296.72160.24320.1367-0.0106-0.1587-0.5569-0.1291-0.02990.26190.31380.27840.10410.00950.13830.01380.018327.8631.48920.109
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 42
2X-RAY DIFFRACTION2A43 - 81
3X-RAY DIFFRACTION3A82 - 131

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